diff --git a/404.html b/404.html
index c0c7cd9..8c88406 100644
--- a/404.html
+++ b/404.html
@@ -20,7 +20,7 @@
 
     <a class="navbar-brand me-2" href="https://waldronlab.io/HGNChelper/index.html">HGNChelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.14</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.15</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/index.html b/articles/index.html
index 2875088..702d155 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -20,7 +20,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">HGNChelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.14</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.15</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -59,7 +59,7 @@ <h1>HGNChelper Introduction</h1>
                         <h4 data-toc-skip class="author">Levi Waldron
 and Markus Riester</h4>
             
-            <h4 data-toc-skip class="date">2024-11-14</h4>
+            <h4 data-toc-skip class="date">2024-11-16</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/waldronlab/HGNChelper/blob/devel/vignettes/index.Rmd" class="external-link"><code>vignettes/index.Rmd</code></a></small>
       <div class="d-none name"><code>index.Rmd</code></div>
@@ -105,7 +105,7 @@ <h2 id="hgnchelper-functionality">HGNChelper functionality<a class="anchor" aria
 <span><span class="va">human</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"FN1"</span>, <span class="st">"tp53"</span>, <span class="st">"UNKNOWNGENE"</span>,<span class="st">"7-Sep"</span>, <span class="st">"9/7"</span>, <span class="st">"1-Mar"</span>, <span class="st">"Oct4"</span>, <span class="st">"4-Oct"</span>,</span>
 <span>      <span class="st">"OCT4-PG4"</span>, <span class="st">"C19ORF71"</span>, <span class="st">"C19orf71"</span><span class="op">)</span></span>
 <span><span class="fu"><a href="../reference/checkGeneSymbols.html">checkGeneSymbols</a></span><span class="op">(</span><span class="va">human</span><span class="op">)</span></span>
-<span><span class="co">#&gt; Maps last updated on: Fri May 17 15:09:37 2024</span></span>
+<span><span class="co">#&gt; Maps last updated on: Sat Nov 16 10:35:32 2024</span></span>
 <span><span class="co">#&gt; Warning in checkGeneSymbols(human): Human gene symbols should be all upper-case</span></span>
 <span><span class="co">#&gt; except for the 'orf' in open reading frames. The case of some letters was</span></span>
 <span><span class="co">#&gt; corrected.</span></span>
@@ -134,7 +134,7 @@ <h2 id="mouse-gene-symbols">Mouse gene symbols<a class="anchor" aria-label="anch
 <code>species=mouse</code>:</p>
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/checkGeneSymbols.html">checkGeneSymbols</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"1-Feb"</span>, <span class="st">"Pzp"</span>, <span class="st">"A2m"</span>, <span class="st">"E430008G22Rik"</span><span class="op">)</span>, species<span class="op">=</span><span class="st">"mouse"</span><span class="op">)</span></span>
-<span><span class="co">#&gt; Maps last updated on: Fri May 17 15:09:37 2024</span></span>
+<span><span class="co">#&gt; Maps last updated on: Sat Nov 16 10:35:32 2024</span></span>
 <span><span class="co">#&gt; Warning in checkGeneSymbols(c("1-Feb", "Pzp", "A2m", "E430008G22Rik"), species</span></span>
 <span><span class="co">#&gt; = "mouse"): x contains non-approved gene symbols</span></span>
 <span><span class="co">#&gt;               x Approved Suggested.Symbol</span></span>
@@ -168,9 +168,9 @@ <h2 id="what-exactly-checkgenesymbols-does">What exactly checkGeneSymbols does<a
 and invalid but mappable symbols, shipped with HGNChelper:</p>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/dim.html" class="external-link">dim</a></span><span class="op">(</span><span class="va">mouse.table</span><span class="op">)</span></span>
-<span><span class="co">#&gt; [1] 752802      2</span></span>
+<span><span class="co">#&gt; [1] 790110      2</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/dim.html" class="external-link">dim</a></span><span class="op">(</span><span class="va">hgnc.table</span><span class="op">)</span></span>
-<span><span class="co">#&gt; [1] 103744      3</span></span></code></pre></div>
+<span><span class="co">#&gt; [1] 103939      3</span></span></code></pre></div>
 <p>These are a combination of manually generated Excel mogrifications
 that remain constant, and aliases that can become out of date with
 time.</p>
@@ -208,21 +208,21 @@ <h2 id="what-does-the-expand-ambiguous-argument-do">What does the expand.ambiguo
 an approved symbol.</p>
 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/checkGeneSymbols.html">checkGeneSymbols</a></span><span class="op">(</span><span class="st">"AAVS1"</span>, expand.ambiguous <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
-<span><span class="co">#&gt; Maps last updated on: Fri May 17 15:09:37 2024</span></span>
+<span><span class="co">#&gt; Maps last updated on: Sat Nov 16 10:35:32 2024</span></span>
 <span><span class="co">#&gt;       x Approved Suggested.Symbol</span></span>
 <span><span class="co">#&gt; 1 AAVS1     TRUE            AAVS1</span></span>
 <span><span class="fu"><a href="../reference/checkGeneSymbols.html">checkGeneSymbols</a></span><span class="op">(</span><span class="st">"AAVS1"</span>, expand.ambiguous <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
-<span><span class="co">#&gt; Maps last updated on: Fri May 17 15:09:37 2024</span></span>
+<span><span class="co">#&gt; Maps last updated on: Sat Nov 16 10:35:32 2024</span></span>
 <span><span class="co">#&gt;       x Approved   Suggested.Symbol</span></span>
 <span><span class="co">#&gt; 1 AAVS1     TRUE AAVS1 /// PPP1R12C</span></span>
 <span></span>
 <span><span class="fu"><a href="../reference/checkGeneSymbols.html">checkGeneSymbols</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Cpamd8"</span>, <span class="st">"Mug2"</span><span class="op">)</span>, species <span class="op">=</span> <span class="st">"mouse"</span>, expand.ambiguous <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
-<span><span class="co">#&gt; Maps last updated on: Fri May 17 15:09:37 2024</span></span>
+<span><span class="co">#&gt; Maps last updated on: Sat Nov 16 10:35:32 2024</span></span>
 <span><span class="co">#&gt;        x Approved Suggested.Symbol</span></span>
 <span><span class="co">#&gt; 1 Cpamd8     TRUE           Cpamd8</span></span>
 <span><span class="co">#&gt; 2   Mug2     TRUE             Mug2</span></span>
 <span><span class="fu"><a href="../reference/checkGeneSymbols.html">checkGeneSymbols</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Cpamd8"</span>, <span class="st">"Mug2"</span><span class="op">)</span>, species <span class="op">=</span> <span class="st">"mouse"</span>, expand.ambiguous <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
-<span><span class="co">#&gt; Maps last updated on: Fri May 17 15:09:37 2024</span></span>
+<span><span class="co">#&gt; Maps last updated on: Sat Nov 16 10:35:32 2024</span></span>
 <span><span class="co">#&gt;        x Approved Suggested.Symbol</span></span>
 <span><span class="co">#&gt; 1 Cpamd8     TRUE  Cpamd8 /// Mug2</span></span>
 <span><span class="co">#&gt; 2   Mug2     TRUE  Mug2 /// Cpamd8</span></span></code></pre></div>
diff --git a/authors.html b/authors.html
index 036ff2d..495ef35 100644
--- a/authors.html
+++ b/authors.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">HGNChelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.14</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.15</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/index.html b/index.html
index 8ec3575..366511a 100644
--- a/index.html
+++ b/index.html
@@ -22,7 +22,7 @@
 
     <a class="navbar-brand me-2" href="index.html">HGNChelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.14</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.15</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/pkgdown.yml b/pkgdown.yml
index d66ecbe..ad81501 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.1.1
 pkgdown_sha: ~
 articles:
   index: index.html
-last_built: 2024-11-14T21:27Z
+last_built: 2024-11-16T15:55Z
 urls:
   reference: https://waldronlab.io/HGNChelper/reference
   article: https://waldronlab.io/HGNChelper/articles
diff --git a/reference/HGNChelper-package.html b/reference/HGNChelper-package.html
index f824351..1b4d08d 100644
--- a/reference/HGNChelper-package.html
+++ b/reference/HGNChelper-package.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">HGNChelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.14</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.15</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/affyToR.html b/reference/affyToR.html
index 57732cb..6487986 100644
--- a/reference/affyToR.html
+++ b/reference/affyToR.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">HGNChelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.14</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.15</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/checkGeneSymbols.html b/reference/checkGeneSymbols.html
index c60bd77..bd4f37c 100644
--- a/reference/checkGeneSymbols.html
+++ b/reference/checkGeneSymbols.html
@@ -15,7 +15,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">HGNChelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.14</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.15</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -122,7 +122,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">human</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"FN1"</span>, <span class="st">"TP53"</span>, <span class="st">"UNKNOWNGENE"</span>,<span class="st">"7-Sep"</span>, <span class="st">"9/7"</span>, <span class="st">"1-Mar"</span>, <span class="st">"Oct4"</span>, <span class="st">"4-Oct"</span>,</span></span>
 <span class="r-in"><span>      <span class="st">"OCT4-PG4"</span>, <span class="st">"C19ORF71"</span>, <span class="st">"C19orf71"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">checkGeneSymbols</span><span class="op">(</span><span class="va">human</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Maps last updated on: Fri May 17 15:09:37 2024</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Maps last updated on: Sat Nov 16 10:35:32 2024</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Human gene symbols should be all upper-case except for the 'orf' in open reading frames. The case of some letters was corrected.</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>x contains non-approved gene symbols</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>              x Approved   Suggested.Symbol</span>
@@ -141,7 +141,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co">## Mouse</span></span></span>
 <span class="r-in"><span><span class="va">mouse</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"1-Feb"</span>, <span class="st">"Pzp"</span>, <span class="st">"A2m"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">checkGeneSymbols</span><span class="op">(</span><span class="va">mouse</span>, species<span class="op">=</span><span class="st">"mouse"</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Maps last updated on: Fri May 17 15:09:37 2024</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Maps last updated on: Sat Nov 16 10:35:32 2024</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>x contains non-approved gene symbols</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>       x Approved Suggested.Symbol</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1 1-Feb    FALSE             Feb1</span>
@@ -153,23 +153,23 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co">## Human</span></span></span>
 <span class="r-in"><span><span class="va">human</span> <span class="op">&lt;-</span> <span class="st">"AAVS1"</span></span></span>
 <span class="r-in"><span><span class="fu">checkGeneSymbols</span><span class="op">(</span><span class="va">human</span>, expand.ambiguous<span class="op">=</span><span class="cn">FALSE</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Maps last updated on: Fri May 17 15:09:37 2024</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Maps last updated on: Sat Nov 16 10:35:32 2024</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>       x Approved Suggested.Symbol</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1 AAVS1     TRUE            AAVS1</span>
 <span class="r-in"><span><span class="fu">checkGeneSymbols</span><span class="op">(</span><span class="va">human</span>, expand.ambiguous<span class="op">=</span><span class="cn">TRUE</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Maps last updated on: Fri May 17 15:09:37 2024</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Maps last updated on: Sat Nov 16 10:35:32 2024</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>       x Approved   Suggested.Symbol</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1 AAVS1     TRUE AAVS1 /// PPP1R12C</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co">## Mouse</span></span></span>
 <span class="r-in"><span><span class="va">mouse</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Cpamd8"</span>, <span class="st">"Mug2"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">checkGeneSymbols</span><span class="op">(</span><span class="va">mouse</span>, species <span class="op">=</span> <span class="st">"mouse"</span>, expand.ambiguous <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Maps last updated on: Fri May 17 15:09:37 2024</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Maps last updated on: Sat Nov 16 10:35:32 2024</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>        x Approved Suggested.Symbol</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1 Cpamd8     TRUE           Cpamd8</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 2   Mug2     TRUE             Mug2</span>
 <span class="r-in"><span><span class="fu">checkGeneSymbols</span><span class="op">(</span><span class="va">mouse</span>, species <span class="op">=</span> <span class="st">"mouse"</span>, expand.ambiguous <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Maps last updated on: Fri May 17 15:09:37 2024</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Maps last updated on: Sat Nov 16 10:35:32 2024</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>        x Approved Suggested.Symbol</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1 Cpamd8     TRUE  Cpamd8 /// Mug2</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 2   Mug2     TRUE  Mug2 /// Cpamd8</span>
diff --git a/reference/findExcelGeneSymbols.html b/reference/findExcelGeneSymbols.html
index 386d4b6..f1a9d04 100644
--- a/reference/findExcelGeneSymbols.html
+++ b/reference/findExcelGeneSymbols.html
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">HGNChelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.14</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.15</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/getCurrentMaps.html b/reference/getCurrentMaps.html
index d1a41ae..b6de39a 100644
--- a/reference/getCurrentMaps.html
+++ b/reference/getCurrentMaps.html
@@ -19,7 +19,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">HGNChelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.14</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.15</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/hgnc.table.html b/reference/hgnc.table.html
index c2d811b..f5dc53d 100644
--- a/reference/hgnc.table.html
+++ b/reference/hgnc.table.html
@@ -21,7 +21,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">HGNChelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.14</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.15</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -65,11 +65,11 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
-    <p>An object of class <code>data.table</code> (inherits from <code>data.frame</code>) with 103744 rows and 3 columns.</p>
+    <p>An object of class <code>data.table</code> (inherits from <code>data.frame</code>) with 103939 rows and 3 columns.</p>
     </div>
     <div class="section level2">
     <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
-    <p>Extracted from <a href="ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/hgnc_complete_set.txt">ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/hgnc_complete_set.txt</a>
+    <p>Extracted from <a href="https://storage.googleapis.com/public-download-files/hgnc/tsv/tsv/hgnc_complete_set.txt" class="external-link">https://storage.googleapis.com/public-download-files/hgnc/tsv/tsv/hgnc_complete_set.txt</a>
 and system.file("extdata/mog_map.csv", package="HGNChelper")</p>
     </div>
 
@@ -80,11 +80,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span>        Symbol Approved.Symbol chromosome</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>        &lt;char&gt;          &lt;char&gt;     &lt;char&gt;</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1:       A1BG            A1BG         19</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2: NCRNA00181        A1BG-AS1         19</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3:   A1BG-AS1        A1BG-AS1         19</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2:   A1BG-AS1        A1BG-AS1         19</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3:   FLJ23569        A1BG-AS1         19</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 4:     A1BGAS        A1BG-AS1         19</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 5:    A1BG-AS        A1BG-AS1         19</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6:   FLJ23569        A1BG-AS1         19</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6: NCRNA00181        A1BG-AS1         19</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/index.html b/reference/index.html
index 82a0917..6f52be1 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">HGNChelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.14</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.15</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/mouse.table.html b/reference/mouse.table.html
index 716de70..6d25891 100644
--- a/reference/mouse.table.html
+++ b/reference/mouse.table.html
@@ -21,7 +21,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">HGNChelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.14</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.15</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -65,7 +65,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
-    <p>An object of class <code>data.frame</code> with 752802 rows and 2 columns.</p>
+    <p>An object of class <code>data.frame</code> with 790110 rows and 2 columns.</p>
     </div>
     <div class="section level2">
     <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
diff --git a/reference/rToAffy.html b/reference/rToAffy.html
index fb2f0bc..77bd72d 100644
--- a/reference/rToAffy.html
+++ b/reference/rToAffy.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">HGNChelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.14</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.15</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/rToSymbol.html b/reference/rToSymbol.html
index f2f7591..21420bd 100644
--- a/reference/rToSymbol.html
+++ b/reference/rToSymbol.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">HGNChelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.14</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.15</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/symbolToR.html b/reference/symbolToR.html
index f165f80..c086bc7 100644
--- a/reference/symbolToR.html
+++ b/reference/symbolToR.html
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">HGNChelper</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.14</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.15</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/search.json b/search.json
index 36d0017..c45d269 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://waldronlab.io/HGNChelper/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Sehyun Oh. Author. Ayush Aggarwal. Author. Markus Riester. Author. Levi Waldron. Author, maintainer.","code":""},{"path":"https://waldronlab.io/HGNChelper/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Sehyun Oh et al. HGNChelper: identification correction invalid gene symbols human mouse. F1000Research 2020, 9:1493. DOI: https://doi.org/10.12688/f1000research.28033.1","code":"@Article{,   entry = {Article},   title = {HGNChelper: identification and correction of invalid gene symbols for human and mouse},   author = {Sehyun Oh and Jasmine Abdelnabi and Ragheed Al-Dulaimi and Ayush Aggarwal and Marcel Ramos and Carmen Rodriguez Cabrera and Tiffany Chan and Sean Davis and Markus Riester and Levi Waldron},   journal = {F1000 Research},   year = {2020},   volume = {9:1493}, }"},{"path":"https://waldronlab.io/HGNChelper/index.html","id":"hgnchelper-identification-and-correction-of-invalid-gene-symbols-for-human-and-mouse","dir":"","previous_headings":"","what":"Identify and Correct Invalid HGNC Human Gene Symbols and MGI Mouse Gene Symbols","title":"Identify and Correct Invalid HGNC Human Gene Symbols and MGI Mouse Gene Symbols","text":"Please cite software: Oh S, Abdelnabi J, Al-Dulaimi R et al. HGNChelper: identification correction invalid gene symbols human mouse. F1000Research 2020, 9:1493 (https://doi.org/10.12688/f1000research.28033.1)","code":""},{"path":"https://waldronlab.io/HGNChelper/index.html","id":"updating","dir":"","previous_headings":"","what":"Updating","title":"Identify and Correct Invalid HGNC Human Gene Symbols and MGI Mouse Gene Symbols","text":"update symbols maps human mouse , download repository run: ./update.sh root directory. Note script uses “roxygen2” R library update documentation. Alternatively, can use updated maps without updating package, see ?getCurrentMaps.","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/HGNChelper-package.html","id":null,"dir":"Reference","previous_headings":"","what":"HGNChelper: Identify and Correct Invalid HGNC Human Gene Symbols and MGI Mouse Gene Symbols — HGNChelper-package","title":"HGNChelper: Identify and Correct Invalid HGNC Human Gene Symbols and MGI Mouse Gene Symbols — HGNChelper-package","text":"Contains functions identifying correcting HGNC human gene symbols MGI mouse gene symbols converted date format Excel, withdrawn, aliased. Also contains functions reversibly converting HGNC symbols valid R names.","code":""},{"path":[]},{"path":"https://waldronlab.io/HGNChelper/reference/HGNChelper-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"HGNChelper: Identify and Correct Invalid HGNC Human Gene Symbols and MGI Mouse Gene Symbols — HGNChelper-package","text":"Maintainer: Levi Waldron lwaldron.research@gmail.com Authors: Sehyun Oh sehyun.oh@sph.cuny.edu Ayush Aggarwal ayush.aggarwal@igib.Markus Riester Markus.riester@novartis.com","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/affyToR.html","id":null,"dir":"Reference","previous_headings":"","what":"Title function to convert Affymetrix probeset identifiers to valid R names — affyToR","title":"Title function to convert Affymetrix probeset identifiers to valid R names — affyToR","text":"function simply prepends \"affy.\" probeset IDs create valid R names.  Reverse operation done rToAffy function.","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/affyToR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Title function to convert Affymetrix probeset identifiers to valid R names — affyToR","text":"","code":"affyToR(x)"},{"path":"https://waldronlab.io/HGNChelper/reference/affyToR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Title function to convert Affymetrix probeset identifiers to valid R names — affyToR","text":"x vector Affymetrix probeset identifiers, identifier may digit.","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/affyToR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Title function to convert Affymetrix probeset identifiers to valid R names — affyToR","text":"character vector simply x \"affy.\" prepended value.","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/checkGeneSymbols.html","id":null,"dir":"Reference","previous_headings":"","what":"Identify outdated or Excel-mogrified gene symbols — checkGeneSymbols","title":"Identify outdated or Excel-mogrified gene symbols — checkGeneSymbols","text":"function identifies gene symbols outdated may mogrified Excel spreadsheet programs. output assigned variable, returns data.frame number rows input, second column indicating whether symbols valid third column corrected gene list.","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/checkGeneSymbols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Identify outdated or Excel-mogrified gene symbols — checkGeneSymbols","text":"","code":"checkGeneSymbols(   x,   chromosome = NULL,   unmapped.as.na = TRUE,   map = NULL,   species = \"human\",   expand.ambiguous = FALSE )"},{"path":"https://waldronlab.io/HGNChelper/reference/checkGeneSymbols.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Identify outdated or Excel-mogrified gene symbols — checkGeneSymbols","text":"x character vector gene symbols check modified outdated values chromosome optional integer vector containing chromosome number gene provided argument x. length input x. Currently, argument implemented human gene cases. unmapped..na TRUE (default), unmapped symbols appear NA Suggested.Symbol column. FALSE, original unmapped symbol kept. map Specify want use default maps provided setting species equal \"mouse\" \"human\". Map can data.frame colnames identical c(\"Symbol\", \"Approved.Symbol\"). default maps can updated running interactive example . species character vector length 1, either \"human\" (default) \"mouse\". NULL, anything \"human\" \"mouse\", map argument must provided. expand.ambiguous FALSE (default), genes multiple mapping map approved symbol correct one. TRUE, genes multiple/ambiguous mapping map symbols linked .","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/checkGeneSymbols.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Identify outdated or Excel-mogrified gene symbols — checkGeneSymbols","text":"function return data.frame number rows input, corrections possible map.","code":""},{"path":[]},{"path":"https://waldronlab.io/HGNChelper/reference/checkGeneSymbols.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Identify outdated or Excel-mogrified gene symbols — checkGeneSymbols","text":"","code":"library(HGNChelper)  ## Human human <- c(\"FN1\", \"TP53\", \"UNKNOWNGENE\",\"7-Sep\", \"9/7\", \"1-Mar\", \"Oct4\", \"4-Oct\",       \"OCT4-PG4\", \"C19ORF71\", \"C19orf71\") checkGeneSymbols(human) #> Maps last updated on: Fri May 17 15:09:37 2024 #> Warning: Human gene symbols should be all upper-case except for the 'orf' in open reading frames. The case of some letters was corrected. #> Warning: x contains non-approved gene symbols #>              x Approved   Suggested.Symbol #> 1          FN1     TRUE                FN1 #> 2         TP53     TRUE               TP53 #> 3  UNKNOWNGENE    FALSE               <NA> #> 4        7-Sep    FALSE            SEPTIN7 #> 5          9/7    FALSE            SEPTIN7 #> 6        1-Mar    FALSE MARCHF1 /// MTARC1 #> 7         Oct4    FALSE             POU5F1 #> 8        4-Oct    FALSE             POU5F1 #> 9     OCT4-PG4    FALSE           POU5F1P4 #> 10    C19ORF71    FALSE            TEKTIP1 #> 11    C19orf71    FALSE            TEKTIP1  ## Mouse mouse <- c(\"1-Feb\", \"Pzp\", \"A2m\") checkGeneSymbols(mouse, species=\"mouse\") #> Maps last updated on: Fri May 17 15:09:37 2024 #> Warning: x contains non-approved gene symbols #>       x Approved Suggested.Symbol #> 1 1-Feb    FALSE             Feb1 #> 2   Pzp     TRUE              Pzp #> 3   A2m     TRUE              A2m  ## expand.ambiguous  ## Human human <- \"AAVS1\" checkGeneSymbols(human, expand.ambiguous=FALSE) #> Maps last updated on: Fri May 17 15:09:37 2024 #>       x Approved Suggested.Symbol #> 1 AAVS1     TRUE            AAVS1 checkGeneSymbols(human, expand.ambiguous=TRUE) #> Maps last updated on: Fri May 17 15:09:37 2024 #>       x Approved   Suggested.Symbol #> 1 AAVS1     TRUE AAVS1 /// PPP1R12C  ## Mouse mouse <- c(\"Cpamd8\", \"Mug2\") checkGeneSymbols(mouse, species = \"mouse\", expand.ambiguous = FALSE) #> Maps last updated on: Fri May 17 15:09:37 2024 #>        x Approved Suggested.Symbol #> 1 Cpamd8     TRUE           Cpamd8 #> 2   Mug2     TRUE             Mug2 checkGeneSymbols(mouse, species = \"mouse\", expand.ambiguous = TRUE) #> Maps last updated on: Fri May 17 15:09:37 2024 #>        x Approved Suggested.Symbol #> 1 Cpamd8     TRUE  Cpamd8 /// Mug2 #> 2   Mug2     TRUE  Mug2 /// Cpamd8  ## Updating the map if (interactive()) {     currentHumanMap <- getCurrentHumanMap()     checkGeneSymbols(human, map=currentHumanMap)      # You should save this if you are going to use it multiple times,        # then load it from file rather than burdening HGNC's servers.     save(hgnc.table, file=\"hgnc.table.rda\", compress=\"bzip2\")     load(\"hgnc.table.rda\")     checkGeneSymbols(human, map=hgnc.table) }"},{"path":"https://waldronlab.io/HGNChelper/reference/findExcelGeneSymbols.html","id":null,"dir":"Reference","previous_headings":"","what":"Title function to identify Excel-mogrified gene symbols — findExcelGeneSymbols","title":"Title function to identify Excel-mogrified gene symbols — findExcelGeneSymbols","text":"function identifies gene symbols may mogrified Excel spreadsheet programs.  output assigned variable, returns vector length symbols mapped mapped.","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/findExcelGeneSymbols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Title function to identify Excel-mogrified gene symbols — findExcelGeneSymbols","text":"","code":"findExcelGeneSymbols(   x,   mog.map = read.csv(system.file(\"extdata/mog_map.csv\", package = \"HGNChelper\"), as.is =     TRUE),   regex = \"impossibletomatch^\" )"},{"path":"https://waldronlab.io/HGNChelper/reference/findExcelGeneSymbols.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Title function to identify Excel-mogrified gene symbols — findExcelGeneSymbols","text":"x Vector gene symbols check mogrified values mog.map Map known mogrifications.  dataframe two columns: original mogrified, containing correct incorrect symbols, respectively. regex Regular expression, recognized base::grep function called ignore.case=TRUE, identify mogrified symbols. default regex match anything. regex examples attempt match Excel-mogrified HGNC human gene symbols. necessary matches corresponding entry mog.map$mogrified; values x matched regex found mog.map$mogrified simply corrected.","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/findExcelGeneSymbols.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Title function to identify Excel-mogrified gene symbols — findExcelGeneSymbols","text":"return value function assigned variable, function return vector length input, corrections possible mog.map made.","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/findExcelGeneSymbols.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Title function to identify Excel-mogrified gene symbols — findExcelGeneSymbols","text":"","code":"## Available maps from this package: human <- read.csv(system.file(\"extdata/mog_map.csv\",                                package = \"HGNChelper\"), as.is=TRUE) mouse <- read.csv(system.file(\"extdata/HGNChelper_mog_map_MGI_AMC_2016_03_30.csv\",                                package = \"HGNChelper\"), as.is=TRUE) ## This regex is based that provided by Zeeberg et al., ##  Mistaken Identifiers: Gene name errors can be introduced ## inadvertently when using Excel in bioinformatics.  BMC ##  Bioinformatics 2004, 5:80. re <- \"[0-9]\\\\-(JAN|FEB|MAR|APR|MAY|JUN|JUL|AUG|SEP|OCT|NOV|DEC)|[0-9]\\\\.[0-9][0-9]E\\\\+[[0-9][0-9]\" findExcelGeneSymbols(c(\"2-Apr\", \"APR2\"), mog.map=human, regex=re) #> Warning: Transmogrified gene symbols found.  Returning the following corrections: 2-Apr to 2-Apr #> [1] \"2-Apr\" \"APR2\"  findExcelGeneSymbols(c(\"1-Feb\", \"Feb1\"), mog.map=mouse) #> Warning: Transmogrified gene symbols found.  Returning the following corrections: 1-Feb to Feb1 #> [1] \"Feb1\" \"Feb1\""},{"path":"https://waldronlab.io/HGNChelper/reference/getCurrentMaps.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the current maps for correcting gene symbols — getCurrentMaps","title":"Get the current maps for correcting gene symbols — getCurrentMaps","text":"Valid human mouse gene symbols can updated frequently. Use functions get current lists valid symbols, can use input map argument checkGeneSymbols. Make sure change default species=\"human\" argument checkGeneSymbols mouse. Use getCurrentHumanMap HGNC human gene symbols https://www.genenames.org/ getCurrentMouseMap MGI mouse gene symbols https://www.informatics.jax.org/downloads/reports/MGI_EntrezGene.rpt.","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/getCurrentMaps.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the current maps for correcting gene symbols — getCurrentMaps","text":"","code":"getCurrentHumanMap() getCurrentMouseMap()"},{"path":"https://waldronlab.io/HGNChelper/reference/getCurrentMaps.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the current maps for correcting gene symbols — getCurrentMaps","text":"data.frame can used map argument checkGeneSymbols function","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/getCurrentMaps.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get the current maps for correcting gene symbols — getCurrentMaps","text":"","code":"if (FALSE) { # \\dontrun{ ## human new.hgnc.table <- getCurrentHumanMap() checkGeneSymbols(c(\"3-Oct\", \"10-3\", \"tp53\"), map=new.hgnc.table)  ## mouse new.mouse.table <- getCurrentMouseMap() ## Set species to NULL or \"mouse\"  checkGeneSymbols(c(\"Gm46568\", \"1-Feb\"), map=new.mouse.table, species=\"mouse\") } # }"},{"path":"https://waldronlab.io/HGNChelper/reference/hgnc.table.html","id":null,"dir":"Reference","previous_headings":"","what":"All current and withdrawn HGNC gene symbols and Excel-mogrified symbols — hgnc.table","title":"All current and withdrawn HGNC gene symbols and Excel-mogrified symbols — hgnc.table","text":"data.frame first column providing gene symbol known alias (including withdrawn symbols), second column providing approved HGNC human gene symbol. Symbol: valid, Excel-mogrified, withdrawn symbols Approved.Symbol: Approved symbols","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/hgnc.table.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"All current and withdrawn HGNC gene symbols and Excel-mogrified symbols — hgnc.table","text":"","code":"hgnc.table"},{"path":"https://waldronlab.io/HGNChelper/reference/hgnc.table.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"All current and withdrawn HGNC gene symbols and Excel-mogrified symbols — hgnc.table","text":"object class data.table (inherits data.frame) 103744 rows 3 columns.","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/hgnc.table.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"All current and withdrawn HGNC gene symbols and Excel-mogrified symbols — hgnc.table","text":"Extracted ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/hgnc_complete_set.txt system.file(\"extdata/mog_map.csv\", package=\"HGNChelper\")","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/hgnc.table.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"All current and withdrawn HGNC gene symbols and Excel-mogrified symbols — hgnc.table","text":"","code":"data(\"hgnc.table\", package=\"HGNChelper\") head(hgnc.table) #>        Symbol Approved.Symbol chromosome #>        <char>          <char>     <char> #> 1:       A1BG            A1BG         19 #> 2: NCRNA00181        A1BG-AS1         19 #> 3:   A1BG-AS1        A1BG-AS1         19 #> 4:     A1BGAS        A1BG-AS1         19 #> 5:    A1BG-AS        A1BG-AS1         19 #> 6:   FLJ23569        A1BG-AS1         19"},{"path":"https://waldronlab.io/HGNChelper/reference/mouse.table.html","id":null,"dir":"Reference","previous_headings":"","what":"All current and withdrawn MGI mouse symbols and Excel-mogrified symbols — mouse.table","title":"All current and withdrawn MGI mouse symbols and Excel-mogrified symbols — mouse.table","text":"data.frame first column providing gene symbol known alias (including withdrawn symbols), second column providing approved MGI mouse gene symbol. Symbol: valid, Excel-mogrified, withdrawn symbols Approved.Symbol: Approved symbols","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/mouse.table.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"All current and withdrawn MGI mouse symbols and Excel-mogrified symbols — mouse.table","text":"","code":"mouse.table"},{"path":"https://waldronlab.io/HGNChelper/reference/mouse.table.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"All current and withdrawn MGI mouse symbols and Excel-mogrified symbols — mouse.table","text":"object class data.frame 752802 rows 2 columns.","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/mouse.table.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"All current and withdrawn MGI mouse symbols and Excel-mogrified symbols — mouse.table","text":"Extracted http://www.informatics.jax.org/downloads/reports/MGI_EntrezGene.rpt system.file(\"extdata/HGNChelper_mog_map_MGI_AMC_2016_03_30.csv\", package=\"HGNChelper\")","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/mouse.table.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"All current and withdrawn MGI mouse symbols and Excel-mogrified symbols — mouse.table","text":"","code":"data(\"mouse.table\", package=\"HGNChelper\") head(mouse.table) #>   Symbol Approved.Symbol #> 1  1-Feb            Feb1 #> 2    2/1            Feb1 #> 3  02/01            Feb1 #> 4   2/01            Feb1 #> 5   02/1            Feb1 #> 6   02-1            Feb1"},{"path":"https://waldronlab.io/HGNChelper/reference/rToAffy.html","id":null,"dir":"Reference","previous_headings":"","what":"Title function to convert the output of affyToR back to the original Affymetrix probeset identifiers. — rToAffy","title":"Title function to convert the output of affyToR back to the original Affymetrix probeset identifiers. — rToAffy","text":"function simply strips \"affy.\" added affyToR function.","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/rToAffy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Title function to convert the output of affyToR back to the original Affymetrix probeset identifiers. — rToAffy","text":"","code":"rToAffy(x)"},{"path":"https://waldronlab.io/HGNChelper/reference/rToAffy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Title function to convert the output of affyToR back to the original Affymetrix probeset identifiers. — rToAffy","text":"x character vector returned affyToR function.","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/rToAffy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Title function to convert the output of affyToR back to the original Affymetrix probeset identifiers. — rToAffy","text":"character vector Affymetrix probeset identifiers.","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/rToSymbol.html","id":null,"dir":"Reference","previous_headings":"","what":"Title function to reverse the conversion made by symbolToR — rToSymbol","title":"Title function to reverse the conversion made by symbolToR — rToSymbol","text":"function reverses actions symbolToR function.","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/rToSymbol.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Title function to reverse the conversion made by symbolToR — rToSymbol","text":"","code":"rToSymbol(x)"},{"path":"https://waldronlab.io/HGNChelper/reference/rToSymbol.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Title function to reverse the conversion made by symbolToR — rToSymbol","text":"x character vector returned symbolToR function.","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/rToSymbol.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Title function to reverse the conversion made by symbolToR — rToSymbol","text":"character vector HGNC gene symbols, general valid R names.","code":""},{"path":[]},{"path":"https://waldronlab.io/HGNChelper/reference/symbolToR.html","id":null,"dir":"Reference","previous_headings":"","what":"Title function to *reversibly* convert HGNC gene symbols to valid R names. — symbolToR","title":"Title function to *reversibly* convert HGNC gene symbols to valid R names. — symbolToR","text":"function reversibly converts HGNC gene symbols valid R names prepending \"symbol.\", making following substitutions: \"-\" \"hyphen\", \"@\" \"ampersand\", \"/\" \"forwardslash\".","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/symbolToR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Title function to *reversibly* convert HGNC gene symbols to valid R names. — symbolToR","text":"","code":"symbolToR(x)"},{"path":"https://waldronlab.io/HGNChelper/reference/symbolToR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Title function to *reversibly* convert HGNC gene symbols to valid R names. — symbolToR","text":"x vector HGNC symbols","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/symbolToR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Title function to *reversibly* convert HGNC gene symbols to valid R names. — symbolToR","text":"vector valid R names, length x, can converted HGNC symbols using rToSymbol function.","code":""},{"path":[]}]
+[{"path":"https://waldronlab.io/HGNChelper/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Sehyun Oh. Author. Ayush Aggarwal. Author. Markus Riester. Author. Levi Waldron. Author, maintainer.","code":""},{"path":"https://waldronlab.io/HGNChelper/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Sehyun Oh et al. HGNChelper: identification correction invalid gene symbols human mouse. F1000Research 2020, 9:1493. DOI: https://doi.org/10.12688/f1000research.28033.1","code":"@Article{,   entry = {Article},   title = {HGNChelper: identification and correction of invalid gene symbols for human and mouse},   author = {Sehyun Oh and Jasmine Abdelnabi and Ragheed Al-Dulaimi and Ayush Aggarwal and Marcel Ramos and Carmen Rodriguez Cabrera and Tiffany Chan and Sean Davis and Markus Riester and Levi Waldron},   journal = {F1000 Research},   year = {2020},   volume = {9:1493}, }"},{"path":"https://waldronlab.io/HGNChelper/index.html","id":"hgnchelper-identification-and-correction-of-invalid-gene-symbols-for-human-and-mouse","dir":"","previous_headings":"","what":"Identify and Correct Invalid HGNC Human Gene Symbols and MGI Mouse Gene Symbols","title":"Identify and Correct Invalid HGNC Human Gene Symbols and MGI Mouse Gene Symbols","text":"Please cite software: Oh S, Abdelnabi J, Al-Dulaimi R et al. HGNChelper: identification correction invalid gene symbols human mouse. F1000Research 2020, 9:1493 (https://doi.org/10.12688/f1000research.28033.1)","code":""},{"path":"https://waldronlab.io/HGNChelper/index.html","id":"updating","dir":"","previous_headings":"","what":"Updating","title":"Identify and Correct Invalid HGNC Human Gene Symbols and MGI Mouse Gene Symbols","text":"update symbols maps human mouse , download repository run: ./update.sh root directory. Note script uses “roxygen2” R library update documentation. Alternatively, can use updated maps without updating package, see ?getCurrentMaps.","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/HGNChelper-package.html","id":null,"dir":"Reference","previous_headings":"","what":"HGNChelper: Identify and Correct Invalid HGNC Human Gene Symbols and MGI Mouse Gene Symbols — HGNChelper-package","title":"HGNChelper: Identify and Correct Invalid HGNC Human Gene Symbols and MGI Mouse Gene Symbols — HGNChelper-package","text":"Contains functions identifying correcting HGNC human gene symbols MGI mouse gene symbols converted date format Excel, withdrawn, aliased. Also contains functions reversibly converting HGNC symbols valid R names.","code":""},{"path":[]},{"path":"https://waldronlab.io/HGNChelper/reference/HGNChelper-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"HGNChelper: Identify and Correct Invalid HGNC Human Gene Symbols and MGI Mouse Gene Symbols — HGNChelper-package","text":"Maintainer: Levi Waldron lwaldron.research@gmail.com Authors: Sehyun Oh sehyun.oh@sph.cuny.edu Ayush Aggarwal ayush.aggarwal@igib.Markus Riester Markus.riester@novartis.com","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/affyToR.html","id":null,"dir":"Reference","previous_headings":"","what":"Title function to convert Affymetrix probeset identifiers to valid R names — affyToR","title":"Title function to convert Affymetrix probeset identifiers to valid R names — affyToR","text":"function simply prepends \"affy.\" probeset IDs create valid R names.  Reverse operation done rToAffy function.","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/affyToR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Title function to convert Affymetrix probeset identifiers to valid R names — affyToR","text":"","code":"affyToR(x)"},{"path":"https://waldronlab.io/HGNChelper/reference/affyToR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Title function to convert Affymetrix probeset identifiers to valid R names — affyToR","text":"x vector Affymetrix probeset identifiers, identifier may digit.","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/affyToR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Title function to convert Affymetrix probeset identifiers to valid R names — affyToR","text":"character vector simply x \"affy.\" prepended value.","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/checkGeneSymbols.html","id":null,"dir":"Reference","previous_headings":"","what":"Identify outdated or Excel-mogrified gene symbols — checkGeneSymbols","title":"Identify outdated or Excel-mogrified gene symbols — checkGeneSymbols","text":"function identifies gene symbols outdated may mogrified Excel spreadsheet programs. output assigned variable, returns data.frame number rows input, second column indicating whether symbols valid third column corrected gene list.","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/checkGeneSymbols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Identify outdated or Excel-mogrified gene symbols — checkGeneSymbols","text":"","code":"checkGeneSymbols(   x,   chromosome = NULL,   unmapped.as.na = TRUE,   map = NULL,   species = \"human\",   expand.ambiguous = FALSE )"},{"path":"https://waldronlab.io/HGNChelper/reference/checkGeneSymbols.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Identify outdated or Excel-mogrified gene symbols — checkGeneSymbols","text":"x character vector gene symbols check modified outdated values chromosome optional integer vector containing chromosome number gene provided argument x. length input x. Currently, argument implemented human gene cases. unmapped..na TRUE (default), unmapped symbols appear NA Suggested.Symbol column. FALSE, original unmapped symbol kept. map Specify want use default maps provided setting species equal \"mouse\" \"human\". Map can data.frame colnames identical c(\"Symbol\", \"Approved.Symbol\"). default maps can updated running interactive example . species character vector length 1, either \"human\" (default) \"mouse\". NULL, anything \"human\" \"mouse\", map argument must provided. expand.ambiguous FALSE (default), genes multiple mapping map approved symbol correct one. TRUE, genes multiple/ambiguous mapping map symbols linked .","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/checkGeneSymbols.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Identify outdated or Excel-mogrified gene symbols — checkGeneSymbols","text":"function return data.frame number rows input, corrections possible map.","code":""},{"path":[]},{"path":"https://waldronlab.io/HGNChelper/reference/checkGeneSymbols.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Identify outdated or Excel-mogrified gene symbols — checkGeneSymbols","text":"","code":"library(HGNChelper)  ## Human human <- c(\"FN1\", \"TP53\", \"UNKNOWNGENE\",\"7-Sep\", \"9/7\", \"1-Mar\", \"Oct4\", \"4-Oct\",       \"OCT4-PG4\", \"C19ORF71\", \"C19orf71\") checkGeneSymbols(human) #> Maps last updated on: Sat Nov 16 10:35:32 2024 #> Warning: Human gene symbols should be all upper-case except for the 'orf' in open reading frames. The case of some letters was corrected. #> Warning: x contains non-approved gene symbols #>              x Approved   Suggested.Symbol #> 1          FN1     TRUE                FN1 #> 2         TP53     TRUE               TP53 #> 3  UNKNOWNGENE    FALSE               <NA> #> 4        7-Sep    FALSE            SEPTIN7 #> 5          9/7    FALSE            SEPTIN7 #> 6        1-Mar    FALSE MARCHF1 /// MTARC1 #> 7         Oct4    FALSE             POU5F1 #> 8        4-Oct    FALSE             POU5F1 #> 9     OCT4-PG4    FALSE           POU5F1P4 #> 10    C19ORF71    FALSE            TEKTIP1 #> 11    C19orf71    FALSE            TEKTIP1  ## Mouse mouse <- c(\"1-Feb\", \"Pzp\", \"A2m\") checkGeneSymbols(mouse, species=\"mouse\") #> Maps last updated on: Sat Nov 16 10:35:32 2024 #> Warning: x contains non-approved gene symbols #>       x Approved Suggested.Symbol #> 1 1-Feb    FALSE             Feb1 #> 2   Pzp     TRUE              Pzp #> 3   A2m     TRUE              A2m  ## expand.ambiguous  ## Human human <- \"AAVS1\" checkGeneSymbols(human, expand.ambiguous=FALSE) #> Maps last updated on: Sat Nov 16 10:35:32 2024 #>       x Approved Suggested.Symbol #> 1 AAVS1     TRUE            AAVS1 checkGeneSymbols(human, expand.ambiguous=TRUE) #> Maps last updated on: Sat Nov 16 10:35:32 2024 #>       x Approved   Suggested.Symbol #> 1 AAVS1     TRUE AAVS1 /// PPP1R12C  ## Mouse mouse <- c(\"Cpamd8\", \"Mug2\") checkGeneSymbols(mouse, species = \"mouse\", expand.ambiguous = FALSE) #> Maps last updated on: Sat Nov 16 10:35:32 2024 #>        x Approved Suggested.Symbol #> 1 Cpamd8     TRUE           Cpamd8 #> 2   Mug2     TRUE             Mug2 checkGeneSymbols(mouse, species = \"mouse\", expand.ambiguous = TRUE) #> Maps last updated on: Sat Nov 16 10:35:32 2024 #>        x Approved Suggested.Symbol #> 1 Cpamd8     TRUE  Cpamd8 /// Mug2 #> 2   Mug2     TRUE  Mug2 /// Cpamd8  ## Updating the map if (interactive()) {     currentHumanMap <- getCurrentHumanMap()     checkGeneSymbols(human, map=currentHumanMap)      # You should save this if you are going to use it multiple times,        # then load it from file rather than burdening HGNC's servers.     save(hgnc.table, file=\"hgnc.table.rda\", compress=\"bzip2\")     load(\"hgnc.table.rda\")     checkGeneSymbols(human, map=hgnc.table) }"},{"path":"https://waldronlab.io/HGNChelper/reference/findExcelGeneSymbols.html","id":null,"dir":"Reference","previous_headings":"","what":"Title function to identify Excel-mogrified gene symbols — findExcelGeneSymbols","title":"Title function to identify Excel-mogrified gene symbols — findExcelGeneSymbols","text":"function identifies gene symbols may mogrified Excel spreadsheet programs.  output assigned variable, returns vector length symbols mapped mapped.","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/findExcelGeneSymbols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Title function to identify Excel-mogrified gene symbols — findExcelGeneSymbols","text":"","code":"findExcelGeneSymbols(   x,   mog.map = read.csv(system.file(\"extdata/mog_map.csv\", package = \"HGNChelper\"), as.is =     TRUE),   regex = \"impossibletomatch^\" )"},{"path":"https://waldronlab.io/HGNChelper/reference/findExcelGeneSymbols.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Title function to identify Excel-mogrified gene symbols — findExcelGeneSymbols","text":"x Vector gene symbols check mogrified values mog.map Map known mogrifications.  dataframe two columns: original mogrified, containing correct incorrect symbols, respectively. regex Regular expression, recognized base::grep function called ignore.case=TRUE, identify mogrified symbols. default regex match anything. regex examples attempt match Excel-mogrified HGNC human gene symbols. necessary matches corresponding entry mog.map$mogrified; values x matched regex found mog.map$mogrified simply corrected.","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/findExcelGeneSymbols.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Title function to identify Excel-mogrified gene symbols — findExcelGeneSymbols","text":"return value function assigned variable, function return vector length input, corrections possible mog.map made.","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/findExcelGeneSymbols.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Title function to identify Excel-mogrified gene symbols — findExcelGeneSymbols","text":"","code":"## Available maps from this package: human <- read.csv(system.file(\"extdata/mog_map.csv\",                                package = \"HGNChelper\"), as.is=TRUE) mouse <- read.csv(system.file(\"extdata/HGNChelper_mog_map_MGI_AMC_2016_03_30.csv\",                                package = \"HGNChelper\"), as.is=TRUE) ## This regex is based that provided by Zeeberg et al., ##  Mistaken Identifiers: Gene name errors can be introduced ## inadvertently when using Excel in bioinformatics.  BMC ##  Bioinformatics 2004, 5:80. re <- \"[0-9]\\\\-(JAN|FEB|MAR|APR|MAY|JUN|JUL|AUG|SEP|OCT|NOV|DEC)|[0-9]\\\\.[0-9][0-9]E\\\\+[[0-9][0-9]\" findExcelGeneSymbols(c(\"2-Apr\", \"APR2\"), mog.map=human, regex=re) #> Warning: Transmogrified gene symbols found.  Returning the following corrections: 2-Apr to 2-Apr #> [1] \"2-Apr\" \"APR2\"  findExcelGeneSymbols(c(\"1-Feb\", \"Feb1\"), mog.map=mouse) #> Warning: Transmogrified gene symbols found.  Returning the following corrections: 1-Feb to Feb1 #> [1] \"Feb1\" \"Feb1\""},{"path":"https://waldronlab.io/HGNChelper/reference/getCurrentMaps.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the current maps for correcting gene symbols — getCurrentMaps","title":"Get the current maps for correcting gene symbols — getCurrentMaps","text":"Valid human mouse gene symbols can updated frequently. Use functions get current lists valid symbols, can use input map argument checkGeneSymbols. Make sure change default species=\"human\" argument checkGeneSymbols mouse. Use getCurrentHumanMap HGNC human gene symbols https://www.genenames.org/ getCurrentMouseMap MGI mouse gene symbols https://www.informatics.jax.org/downloads/reports/MGI_EntrezGene.rpt.","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/getCurrentMaps.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the current maps for correcting gene symbols — getCurrentMaps","text":"","code":"getCurrentHumanMap() getCurrentMouseMap()"},{"path":"https://waldronlab.io/HGNChelper/reference/getCurrentMaps.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the current maps for correcting gene symbols — getCurrentMaps","text":"data.frame can used map argument checkGeneSymbols function","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/getCurrentMaps.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get the current maps for correcting gene symbols — getCurrentMaps","text":"","code":"if (FALSE) { # \\dontrun{ ## human new.hgnc.table <- getCurrentHumanMap() checkGeneSymbols(c(\"3-Oct\", \"10-3\", \"tp53\"), map=new.hgnc.table)  ## mouse new.mouse.table <- getCurrentMouseMap() ## Set species to NULL or \"mouse\"  checkGeneSymbols(c(\"Gm46568\", \"1-Feb\"), map=new.mouse.table, species=\"mouse\") } # }"},{"path":"https://waldronlab.io/HGNChelper/reference/hgnc.table.html","id":null,"dir":"Reference","previous_headings":"","what":"All current and withdrawn HGNC gene symbols and Excel-mogrified symbols — hgnc.table","title":"All current and withdrawn HGNC gene symbols and Excel-mogrified symbols — hgnc.table","text":"data.frame first column providing gene symbol known alias (including withdrawn symbols), second column providing approved HGNC human gene symbol. Symbol: valid, Excel-mogrified, withdrawn symbols Approved.Symbol: Approved symbols","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/hgnc.table.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"All current and withdrawn HGNC gene symbols and Excel-mogrified symbols — hgnc.table","text":"","code":"hgnc.table"},{"path":"https://waldronlab.io/HGNChelper/reference/hgnc.table.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"All current and withdrawn HGNC gene symbols and Excel-mogrified symbols — hgnc.table","text":"object class data.table (inherits data.frame) 103939 rows 3 columns.","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/hgnc.table.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"All current and withdrawn HGNC gene symbols and Excel-mogrified symbols — hgnc.table","text":"Extracted https://storage.googleapis.com/public-download-files/hgnc/tsv/tsv/hgnc_complete_set.txt system.file(\"extdata/mog_map.csv\", package=\"HGNChelper\")","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/hgnc.table.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"All current and withdrawn HGNC gene symbols and Excel-mogrified symbols — hgnc.table","text":"","code":"data(\"hgnc.table\", package=\"HGNChelper\") head(hgnc.table) #>        Symbol Approved.Symbol chromosome #>        <char>          <char>     <char> #> 1:       A1BG            A1BG         19 #> 2:   A1BG-AS1        A1BG-AS1         19 #> 3:   FLJ23569        A1BG-AS1         19 #> 4:     A1BGAS        A1BG-AS1         19 #> 5:    A1BG-AS        A1BG-AS1         19 #> 6: NCRNA00181        A1BG-AS1         19"},{"path":"https://waldronlab.io/HGNChelper/reference/mouse.table.html","id":null,"dir":"Reference","previous_headings":"","what":"All current and withdrawn MGI mouse symbols and Excel-mogrified symbols — mouse.table","title":"All current and withdrawn MGI mouse symbols and Excel-mogrified symbols — mouse.table","text":"data.frame first column providing gene symbol known alias (including withdrawn symbols), second column providing approved MGI mouse gene symbol. Symbol: valid, Excel-mogrified, withdrawn symbols Approved.Symbol: Approved symbols","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/mouse.table.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"All current and withdrawn MGI mouse symbols and Excel-mogrified symbols — mouse.table","text":"","code":"mouse.table"},{"path":"https://waldronlab.io/HGNChelper/reference/mouse.table.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"All current and withdrawn MGI mouse symbols and Excel-mogrified symbols — mouse.table","text":"object class data.frame 790110 rows 2 columns.","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/mouse.table.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"All current and withdrawn MGI mouse symbols and Excel-mogrified symbols — mouse.table","text":"Extracted http://www.informatics.jax.org/downloads/reports/MGI_EntrezGene.rpt system.file(\"extdata/HGNChelper_mog_map_MGI_AMC_2016_03_30.csv\", package=\"HGNChelper\")","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/mouse.table.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"All current and withdrawn MGI mouse symbols and Excel-mogrified symbols — mouse.table","text":"","code":"data(\"mouse.table\", package=\"HGNChelper\") head(mouse.table) #>   Symbol Approved.Symbol #> 1  1-Feb            Feb1 #> 2    2/1            Feb1 #> 3  02/01            Feb1 #> 4   2/01            Feb1 #> 5   02/1            Feb1 #> 6   02-1            Feb1"},{"path":"https://waldronlab.io/HGNChelper/reference/rToAffy.html","id":null,"dir":"Reference","previous_headings":"","what":"Title function to convert the output of affyToR back to the original Affymetrix probeset identifiers. — rToAffy","title":"Title function to convert the output of affyToR back to the original Affymetrix probeset identifiers. — rToAffy","text":"function simply strips \"affy.\" added affyToR function.","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/rToAffy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Title function to convert the output of affyToR back to the original Affymetrix probeset identifiers. — rToAffy","text":"","code":"rToAffy(x)"},{"path":"https://waldronlab.io/HGNChelper/reference/rToAffy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Title function to convert the output of affyToR back to the original Affymetrix probeset identifiers. — rToAffy","text":"x character vector returned affyToR function.","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/rToAffy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Title function to convert the output of affyToR back to the original Affymetrix probeset identifiers. — rToAffy","text":"character vector Affymetrix probeset identifiers.","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/rToSymbol.html","id":null,"dir":"Reference","previous_headings":"","what":"Title function to reverse the conversion made by symbolToR — rToSymbol","title":"Title function to reverse the conversion made by symbolToR — rToSymbol","text":"function reverses actions symbolToR function.","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/rToSymbol.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Title function to reverse the conversion made by symbolToR — rToSymbol","text":"","code":"rToSymbol(x)"},{"path":"https://waldronlab.io/HGNChelper/reference/rToSymbol.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Title function to reverse the conversion made by symbolToR — rToSymbol","text":"x character vector returned symbolToR function.","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/rToSymbol.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Title function to reverse the conversion made by symbolToR — rToSymbol","text":"character vector HGNC gene symbols, general valid R names.","code":""},{"path":[]},{"path":"https://waldronlab.io/HGNChelper/reference/symbolToR.html","id":null,"dir":"Reference","previous_headings":"","what":"Title function to *reversibly* convert HGNC gene symbols to valid R names. — symbolToR","title":"Title function to *reversibly* convert HGNC gene symbols to valid R names. — symbolToR","text":"function reversibly converts HGNC gene symbols valid R names prepending \"symbol.\", making following substitutions: \"-\" \"hyphen\", \"@\" \"ampersand\", \"/\" \"forwardslash\".","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/symbolToR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Title function to *reversibly* convert HGNC gene symbols to valid R names. — symbolToR","text":"","code":"symbolToR(x)"},{"path":"https://waldronlab.io/HGNChelper/reference/symbolToR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Title function to *reversibly* convert HGNC gene symbols to valid R names. — symbolToR","text":"x vector HGNC symbols","code":""},{"path":"https://waldronlab.io/HGNChelper/reference/symbolToR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Title function to *reversibly* convert HGNC gene symbols to valid R names. — symbolToR","text":"vector valid R names, length x, can converted HGNC symbols using rToSymbol function.","code":""},{"path":[]}]