Update package anchors for Rd \link{} targets

man/RNAseqdata.Rd

@@ -52,8 +52,8 @@ using the
   \code{"vst"} for variance stabilizing transformation. If missing, default value
   defined at \code{"rlog"} for datasets with less than 30 samples and at \code{"vst"} if not}
 
-\item{transfo.blind}{Argument given to function \code{\link{rlog}} or \code{\link{vst}},
-  see \code{\link{rlog}} and \code{\link{vst}} for an explaination, by default
+\item{transfo.blind}{Argument given to function \code{\link[DESeq2]{rlog}} or \code{\link[DESeq2]{vst}},
+  see \code{\link[DESeq2]{rlog}} and \code{\link[DESeq2]{vst}} for an explaination, by default
   at \code{TRUE} as in the \code{DESeq2} package .}
 
 \item{round.counts}{Put it to TRUE if your counts come from Kallisto or Salmon
@@ -76,7 +76,7 @@ of data) and gives in the \code{print} information
 that should help the user to check that the coding of data is correct : the tested doses (or concentrations) 
 the number of replicates for each dose, the number of items, the identifiers 
 of the first 20 items. Data are normalized with respect to library size
-and tranformed using functions \code{\link{rlog}} or \code{\link{vst}} of the 
+and tranformed using functions \code{\link[DESeq2]{rlog}} or \code{\link[DESeq2]{vst}} of the 
 \code{DESeq2} package depending on the specified method : \code{"rlog"} 
 (recommended default choice) or 
 \code{"vst"}.
@@ -122,7 +122,7 @@ and tranformed using functions \code{\link{rlog}} or \code{\link{vst}} of the
 
 \seealso{
     See \code{\link{read.table}} the function used to import data,
-    \code{\link{rlog}} and \code{\link{vst}} for details about the 
+    \code{\link[DESeq2]{rlog}} and \code{\link[DESeq2]{vst}} for details about the 
     transformation methods and 
     \code{\link{microarraydata}}, \code{\link{continuousomicdata}} and
     \code{\link{continuousanchoringdata}} for other types of data.

man/itemselect.Rd

@@ -42,13 +42,13 @@ an ANOVA-type test (see details for further explaination).}
 The selection of responsive items is performed using the \code{limma} package
 for microarray and continuous omics data (such as metabolomics), the \code{DESeq2} package for
 RNAseq data and the \code{lm} function for continuous anchoring data. 
-Three methods are proposed (as described below). Within \code{limma} those methods are implemented using functions \code{\link{lmFit}},  
-\code{\link{eBayes}} and \code{\link{topTable}} with p-values ajusted for multiple 
+Three methods are proposed (as described below). Within \code{limma} those methods are implemented using functions \code{\link[limma]{lmFit}},  
+\code{\link[limma]{eBayes}} and \code{\link[limma]{topTable}} with p-values ajusted for multiple 
 testing using the Benjamini-Hochberg method (also called q-values), with the false discovery rate given in
 input (argument \code{FDR}). 
 Within \code{DESeq2} those methods
-are implemented using functions \code{\link{DESeqDataSetFromMatrix}},  
-\code{\link{DESeq}} and \code{\link{results}} with p-values ajusted for multiple 
+are implemented using functions \code{\link[DESeq2]{DESeqDataSetFromMatrix}},  
+\code{\link[DESeq2]{DESeq}} and \code{\link[DESeq2]{results}} with p-values ajusted for multiple 
 testing using the Benjamini-Hochberg method (also called q-values), with the false discovery rate given in
 input (argument \code{FDR}). 
 For continuous anchoring data, the \code{lm} and \code{anova} functions are used 
@@ -100,10 +100,10 @@ All items having a proportion of such tied minimal values above the input argume
 }
 
 \seealso{
-    See \code{\link{lmFit}}, \code{\link{eBayes}} and \code{\link{topTable}}
+    See \code{\link[limma]{lmFit}}, \code{\link[limma]{eBayes}} and \code{\link[limma]{topTable}}
     for details about the used functions of the \code{limma} package and 
-    \code{\link{DESeqDataSetFromMatrix}},
-    \code{\link{DESeq}} and \code{\link{results}}
+    \code{\link[DESeq2]{DESeqDataSetFromMatrix}},
+    \code{\link[DESeq2]{DESeq}} and \code{\link[DESeq2]{results}}
     for details about the used functions of the \code{DESeq2} package.
 }
 

man/microarraydata.Rd

@@ -50,7 +50,7 @@ of \code{read.table(file, header = FALSE)} on a file described as above. }
 \item{check}{If TRUE the format of the input file is checked.}
 
 \item{norm.method}{If \code{"none"} no normalization is performed, else a 
-normalization is performed using the function normalizeBetweenArrays of the 
+normalization is performed using the function \code{normalizeBetweenArrays} of the 
 \code{limma} package using the specified method.}
 
 \item{x}{An object of class \code{"microarraydata"}.}
@@ -69,7 +69,7 @@ of data) and gives in the \code{print} information
 that should help the user to check that the coding of data is correct : the tested doses (or concentrations) 
 the number of replicates for each dose, the number of items, the identifiers 
 of the first 20 items. If the argument \code{norm.method} is not \code{"none"},
-data are normalized using the function \code{\link{normalizeBetweenArrays}} of the 
+data are normalized using the function \code{\link[limma]{normalizeBetweenArrays}} of the 
 \code{limma} package using the specified method : \code{"cyclicloess"} (default choice), 
 \code{"quantile"} or \code{"scale"}.
 }
@@ -112,7 +112,7 @@ data are normalized using the function \code{\link{normalizeBetweenArrays}} of t
 
 \seealso{
     See \code{\link{read.table}} the function used to import data, 
-    \code{\link{normalizeBetweenArrays}} for details about the normalization and 
+    \code{\link[limma]{normalizeBetweenArrays}} for details about the normalization and 
     \code{\link{RNAseqdata}}, \code{\link{continuousomicdata}} and
     \code{\link{continuousanchoringdata}} for other types of data.}