Built site for gh-pages

.nojekyll

@@ -1 +1 @@
-f5e4c4b9
+36ac1e8f

index-preview.html

@@ -1986,7 +1986,7 @@ <h2 class="unnumbered anchored" data-anchor-id="references">References</h2>
     }
   }
 });
-</script>  </div> <!-- /content -->  <script>var lightboxQuarto = GLightbox({"openEffect":"zoom","descPosition":"bottom","selector":".lightbox","loop":false,"closeEffect":"zoom"});
+</script>  </div> <!-- /content -->  <script>var lightboxQuarto = GLightbox({"openEffect":"zoom","loop":false,"closeEffect":"zoom","descPosition":"bottom","selector":".lightbox"});
 window.onload = () => {
   lightboxQuarto.on('slide_before_load', (data) => {
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index.html

@@ -974,7 +974,7 @@ <h2 class="unnumbered anchored" data-anchor-id="references">References</h2>
 });
 </script>
 </div> <!-- /content -->
-<script>var lightboxQuarto = GLightbox({"openEffect":"zoom","loop":false,"descPosition":"bottom","selector":".lightbox","closeEffect":"zoom"});
+<script>var lightboxQuarto = GLightbox({"selector":".lightbox","closeEffect":"zoom","loop":false,"openEffect":"zoom","descPosition":"bottom"});
 window.onload = () => {
   lightboxQuarto.on('slide_before_load', (data) => {
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notebooks/TCGA-preview.html

@@ -225,12 +225,10 @@ <h2 id="toc-title">Table of contents</h2>
 <span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a>  <span class="at">warning =</span> <span class="cn">FALSE</span>,</span>
 <span id="cb3-3"><a href="#cb3-3" aria-hidden="true" tabindex="-1"></a>  <span class="at">message =</span> <span class="cn">FALSE</span>,</span>
 <span id="cb3-4"><a href="#cb3-4" aria-hidden="true" tabindex="-1"></a>  <span class="at">dpi =</span> <span class="dv">180</span>,</span>
-<span id="cb3-5"><a href="#cb3-5" aria-hidden="true" tabindex="-1"></a>  <span class="at">fig.width =</span> <span class="dv">15</span>,</span>
-<span id="cb3-6"><a href="#cb3-6" aria-hidden="true" tabindex="-1"></a>  <span class="at">fig.height =</span> <span class="dv">8</span>,</span>
-<span id="cb3-7"><a href="#cb3-7" aria-hidden="true" tabindex="-1"></a>  <span class="at">echo =</span> <span class="cn">TRUE</span></span>
-<span id="cb3-8"><a href="#cb3-8" aria-hidden="true" tabindex="-1"></a>)</span>
-<span id="cb3-9"><a href="#cb3-9" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb3-10"><a href="#cb3-10" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(tidyverse)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<span id="cb3-5"><a href="#cb3-5" aria-hidden="true" tabindex="-1"></a>  <span class="at">echo =</span> <span class="cn">TRUE</span></span>
+<span id="cb3-6"><a href="#cb3-6" aria-hidden="true" tabindex="-1"></a>)</span>
+<span id="cb3-7"><a href="#cb3-7" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb3-8"><a href="#cb3-8" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(tidyverse)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stderr">
 <pre><code>Warning: package 'ggplot2' was built under R version 4.3.2</code></pre>
 </div>

notebooks/TCGA.embed.ipynb

@@ -8,7 +8,7 @@
     "\n",
     "Analysis of Mutation Data from The Cancer Genome Atlas (TCGA)"
    ],
-   "id": "7d05cb47-3d1f-484b-839d-5530ee7ff891"
+   "id": "574aa135-2d60-40a4-8441-cb21a6ad25a4"
   },
   {
    "cell_type": "code",
@@ -92,7 +92,7 @@
     "#| include: false\n",
     "library(knitr)"
    ],
-   "id": "e0a57f50-7594-4c67-ab9b-85e1d8d6f93a"
+   "id": "46c80529-9dea-4bde-b5d0-5a7a96e1baec"
   },
   {
    "cell_type": "markdown",
@@ -106,7 +106,7 @@
     "\n",
     "First, let’s load the packages needed."
    ],
-   "id": "f2d0810b-20f0-47e6-8068-bdf4fb54ccb0"
+   "id": "523b3ed6-fa85-43ad-afb4-f3713375452f"
   },
   {
    "cell_type": "code",
@@ -474,7 +474,7 @@
    "source": [
     "library(curatedTCGAData)"
    ],
-   "id": "b367700c-0e71-48c9-ad8f-9167be259e57"
+   "id": "0b32b15c-969f-4bda-afe7-1f66cc3f1240"
   },
   {
    "cell_type": "markdown",
@@ -486,7 +486,7 @@
     "\n",
     "In this specific case, we are gonna work with RNA-Seq data, mutation data and methylation data from Rectum Adenocarcinoma (READ). The clinical data is included by default."
    ],
-   "id": "35451ee3-22e3-4303-9158-06dd1d40b081"
+   "id": "4c8ee72f-4b83-44d1-8a21-2c33c8fbf632"
   },
   {
    "cell_type": "code",
@@ -872,7 +872,7 @@
     "                           c(\"RNASeq2GeneNorm\", \"Mutation\", \"Methylation_methyl450\"), \n",
     "                           dry.run = FALSE, version = \"2.1.1\")"
    ],
-   "id": "54f156d0-cf73-443f-8971-f6fdccdfb4b4"
+   "id": "29429639-a37b-49de-9d2e-b7fd2d755543"
   },
   {
    "cell_type": "markdown",
@@ -882,7 +882,7 @@
     "\n",
     "We can see which patients have data for each assay. The assay column gives the experiment type, the primary column gives the unique patient ID and the colname gives the sample ID used as a identifier within a given experiment."
    ],
-   "id": "cffb2903-5322-47a1-a13e-a34fdcc9145f"
+   "id": "23c3ca92-1e6e-4589-b937-36f8e1eeef80"
   },
   {
    "cell_type": "code",
@@ -913,15 +913,15 @@
    "source": [
     "sampleMap(readData)"
    ],
-   "id": "8bd6d649-7bcc-4dd0-afd4-7cc0e310ea88"
+   "id": "116f6b70-f233-4620-8bd0-c6dceffc80df"
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "Not all patients have data for all assays, and some of them can have multiple data entries for one or more experiment type. This may correspond to multiple biopsies or matched tumor and normal samples from an individual patient."
    ],
-   "id": "2944e649-ef92-411a-92e4-29f3fb254396"
+   "id": "d8132180-0b52-4512-b5be-46d94a8343c4"
   },
   {
    "cell_type": "code",
@@ -945,15 +945,15 @@
     "  table() |> \n",
     "  table()"
    ],
-   "id": "9c6bfa1c-0bcf-4f71-a96b-57bed88de589"
+   "id": "4e12c0d0-2f8b-45f6-92c0-c59ebb294dbf"
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "We can see the metadata of the patients with `colData`. Note that there are more than 2000 columns of data per patient (not necessarily complete)."
    ],
-   "id": "33bcadee-d1cd-4c79-bff8-a1e408479f16"
+   "id": "9fac6925-bec3-4e7f-b0d6-09c486a61db2"
   },
   {
    "cell_type": "code",
@@ -983,15 +983,15 @@
     "  as_tibble()\n",
     "dim(clin)"
    ],
-   "id": "1eb740f3-9cee-40e0-9c16-aec799ce1cdc"
+   "id": "4bb6a39a-0853-4e23-b051-3af9b7c808fa"
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "As an example, for rectum adenocarcinoma, we can see the tumor stage."
    ],
-   "id": "5ae40e12-9df3-4068-80cc-b642e82b6eff"
+   "id": "ed50c735-247e-4b7f-920d-37ae8acabf27"
   },
   {
    "cell_type": "code",
@@ -1013,15 +1013,15 @@
     "  pull(pathology_T_stage) |> \n",
     "  table()"
    ],
-   "id": "528461b9-60ee-4f35-bb36-ff3f210ec1e2"
+   "id": "3515cd8d-ec67-48ee-8064-5a1841333ad9"
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "Stage T4 have subgroups. To simplify the analysis, let’s combine all T4 tumors."
    ],
-   "id": "ec490fc3-25a7-4c5a-be3f-2301576280b1"
+   "id": "d171e769-98d5-4012-81a6-0c4faa955761"
   },
   {
    "cell_type": "code",
@@ -1048,15 +1048,15 @@
     "clin$t_stage |> \n",
     "  table()"
    ],
-   "id": "baa0eb4f-4c76-40be-bd37-2ce87148cc87"
+   "id": "9ba65abf-887d-4d5f-83f0-e7c7eef525fd"
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "Also, we can see the vital status (alive=0, deceased=1)"
    ],
-   "id": "c4bd395d-e22c-4bc0-8ac7-68847a77a2ae"
+   "id": "aaa14215-a737-45e0-b49e-cc9a35792401"
   },
   {
    "cell_type": "code",
@@ -1077,15 +1077,15 @@
     "clin$vital_status |> \n",
     "  table()"
    ],
-   "id": "e8853f0a-bfce-4142-a082-8d22a59cb90d"
+   "id": "7b6bebd3-87fa-4981-83ff-7195117929ad"
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "Or combine tumor status and vital status."
    ],
-   "id": "3da5bfc6-1b09-49f7-a40e-16048724a17e"
+   "id": "3d2b747c-f1eb-45b1-9907-c5b58fa8ae18"
   },
   {
    "cell_type": "code",
@@ -1108,7 +1108,7 @@
    "source": [
     "table(clin$t_stage, clin$vital_status)"
    ],
-   "id": "e91b9455-01ad-4ada-9633-a8bb0719f044"
+   "id": "04e5551f-8d28-46d2-a76b-3b3f9c77d070"
   },
   {
    "cell_type": "markdown",
@@ -1118,7 +1118,7 @@
     "\n",
     "Let’s begin analyzing the mutation data. Below is the code to retrieve the mutation data."
    ],
-   "id": "47d0d340-a475-4ecd-a2b3-57a18d77c031"
+   "id": "2033ee9f-7fcb-4b04-bd6d-eaa0d7a03a3c"
   },
   {
    "cell_type": "code",
@@ -1144,15 +1144,15 @@
     "\n",
     "mut_data"
    ],
-   "id": "4dfa8d89-7c44-49ca-a8b8-3f4a2d3d89c8"
+   "id": "a296ef66-0e67-4562-9c96-7183778b6432"
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "From the inspection of the sample IDs we can see that the mutation colnames match to the **primary** column from he clinical data."
    ],
-   "id": "b9fcb7b8-7abd-44a2-9423-2a5a3a069488"
+   "id": "8f501866-ce26-439f-9c54-f5b68874290f"
   },
   {
    "cell_type": "code",
@@ -1181,15 +1181,15 @@
     "mut_sample_ids = colnames(mut_data)\n",
     "head(mut_sample_ids)"
    ],
-   "id": "261b5f42-e277-498f-849a-8a193cac1a26"
+   "id": "1fd7ca43-6209-4519-82b8-b8db63ee5d80"
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "We need to manipulate these by substracting 12 characters."
    ],
-   "id": "28d0c92a-3675-47f6-8aa0-d22cc4511791"
+   "id": "52066818-c5a2-450d-9a8f-50100cf07e2b"
   },
   {
    "cell_type": "code",
@@ -1210,15 +1210,15 @@
     "\n",
     "all(mut_sample_ids %in% clin$patientID)"
    ],
-   "id": "cf1edb90-bb34-4e77-b5ec-d98905850acf"
+   "id": "f84ea1ef-32d9-4992-84bf-6077917b7fbd"
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "Is important to note that the data stored in `assay(mut_data)` is difficult to work with because is a sparse matrix that has a row for each `GRanges` with a mutation in at least one sample."
    ],
-   "id": "83acdaa5-c1ee-4898-a742-ba616bc59e0d"
+   "id": "9b33fb78-4dcd-40ff-8c6c-e78835fc6317"
   },
   {
    "cell_type": "code",
@@ -1252,15 +1252,15 @@
    "source": [
     "assay(mut_data)[1:3,1:3]"
    ],
-   "id": "cb3a519e-56f2-4be7-8f40-845972b18121"
+   "id": "113cb8c4-eadc-4e0e-9267-e8a5f61b224b"
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "We can get more information if we look at the mutation information for each patient."
    ],
-   "id": "2fe50af5-5d1b-4019-ba05-bc8fc0875c1f"
+   "id": "d4936f94-97a9-4ed4-a0b4-76d1acb7cdfa"
   },
   {
    "cell_type": "code",
@@ -1433,15 +1433,15 @@
     "\n",
     "mut_assay # GRangesList"
    ],
-   "id": "8f38aaa0-7e91-4a4c-a4fb-d5901aab7db3"
+   "id": "bf4855bc-4c23-450c-8cb9-ccf7e853dc1f"
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "Let’s inspect the data from the first patient. We can see from the metadata information the Hugo Symbol, mutation status and predicted effect of each mutation at variant classification."
    ],
-   "id": "7bfe0955-25bf-4557-8df9-667ead078e65"
+   "id": "6f861f57-00b8-43ca-b470-26a54a77ca75"
   },
   {
    "cell_type": "code",
@@ -1626,15 +1626,15 @@
    "source": [
     "mut_assay[[1]]"
    ],
-   "id": "7f3acc8c-5848-4ab1-80fe-f67e9760e95a"
+   "id": "5c70092e-f261-4065-9738-8555bd4bc7bc"
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "Now, is kind of a trouble to inspect manually each patient. So, lets get all mutation information from Hugo symbol and Variant classification for all the patients."
    ],
-   "id": "7784b978-1f18-4c95-bfcc-24e6006faf1e"
+   "id": "5c6bf792-f31c-4d40-a9b5-a2687b9d9c33"
   },
   {
    "cell_type": "code",
@@ -1675,15 +1675,15 @@
     "\n",
     "head(var_class_df)"
    ],
-   "id": "7dc9665f-6748-4c28-b541-0689b0d8ed70"
+   "id": "ff466972-3bae-4825-85c8-dcf3f96a9670"
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "We can visualize the most common mutated genes genes in rectum adenocarcinoma"
    ],
-   "id": "d24e2a8c-3980-4cf2-8205-b79da31ff0f1"
+   "id": "0553f3cd-4e84-401a-8c19-de7179ee1835"
   }
  ],
  "nbformat": 4,