diff --git a/DESCRIPTION b/DESCRIPTION index 8291f24..29a9b77 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -39,12 +39,13 @@ Suggests: rmarkdown License: GPL-3 Encoding: UTF-8 +Additional_repositories: https://bedapub.r-universe.dev URL: https://github.com/bedapub/ribiosExpression BugReports: https://github.com/bedapub/ribiosExpression/issues biocViews: GeneExpression, DifferentialExpression, Microarray, DataImport, Visualization VignetteBuilder: knitr -RoxygenNote: 7.3.2 +RoxygenNote: 7.3.3 Collate: 'AllClasses.R' 'AllGenerics.R' @@ -75,7 +76,7 @@ Collate: 'writeVarMetadata.R' Remotes: github::bedapub/ribiosIO, - github::bedapub/ribiosUtils, github::bedapub/ribiosPlot, github::bedapub/ribiosArg, github::bedapub/ribiosAnnotation + diff --git a/NAMESPACE b/NAMESPACE index b7b204d..99ea3c2 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -64,9 +64,6 @@ exportClasses(DesignContrast) exportMethods("contrastAnnotation<-") exportMethods("contrastMatrix<-") exportMethods("designMatrix<-") -exportMethods(`contrastAnnotation<-`) -exportMethods(`contrastMatrix<-`) -exportMethods(`designMatrix<-`) exportMethods(annotate) exportMethods(contrastAnnotation) exportMethods(contrastMatrix) diff --git a/man/contrastAnnotation-set.Rd b/man/contrastAnnotation-set.Rd index a2dd1bc..5d29b76 100644 --- a/man/contrastAnnotation-set.Rd +++ b/man/contrastAnnotation-set.Rd @@ -2,15 +2,18 @@ % Please edit documentation in R/AllGenerics.R \name{contrastAnnotation<-} \alias{contrastAnnotation<-} -\title{Assign contrast annotaiton to an object} +\title{Assign contrast annotation to an object} \usage{ contrastAnnotation(object) <- value } \arguments{ \item{object}{An object, see supported methods below} -\item{value}{Contrast anaotation data.frame} +\item{value}{Contrast annotation data.frame} +} +\value{ +The modified object } \description{ -Assign contrast annotaiton to an object +Assign contrast annotation to an object } diff --git a/man/contrastAnnotation.Rd b/man/contrastAnnotation.Rd index 5462163..74cf994 100644 --- a/man/contrastAnnotation.Rd +++ b/man/contrastAnnotation.Rd @@ -17,6 +17,9 @@ contrastAnnotation(object) \item{value}{A contrast annotation data.frame} } +\value{ +A data.frame annotating contrasts +} \description{ Extract the contrast annotation data.frame from an object } diff --git a/man/contrastMatrix-set.Rd b/man/contrastMatrix-set.Rd index 23a270c..6c49996 100644 --- a/man/contrastMatrix-set.Rd +++ b/man/contrastMatrix-set.Rd @@ -11,6 +11,9 @@ contrastMatrix(object) <- value \item{value}{Contrast matrix} } +\value{ +The modified object +} \description{ Assign contrast matrix to an object } diff --git a/man/contrastMatrix.Rd b/man/contrastMatrix.Rd index 9e7af1e..71f9246 100644 --- a/man/contrastMatrix.Rd +++ b/man/contrastMatrix.Rd @@ -20,6 +20,9 @@ contrastMatrix(object) \item{value}{A contrast matrix} } +\value{ +A numeric contrast matrix +} \description{ Extract the contrast matrix from an object } diff --git a/man/contrastNames.Rd b/man/contrastNames.Rd index 6bed601..98e2cf8 100644 --- a/man/contrastNames.Rd +++ b/man/contrastNames.Rd @@ -15,6 +15,9 @@ contrastNames(object) \arguments{ \item{object}{An object, see supported methods below} } +\value{ +A character vector of contrast names +} \description{ Extract contrastNames from an object } diff --git a/man/designMatrix-set.Rd b/man/designMatrix-set.Rd index 2d38e1c..6415ac7 100644 --- a/man/designMatrix-set.Rd +++ b/man/designMatrix-set.Rd @@ -11,6 +11,9 @@ designMatrix(object) <- value \item{value}{Design matrix} } +\value{ +The modified object +} \description{ Assign design matrix to an object } diff --git a/man/designMatrix.Rd b/man/designMatrix.Rd index e06d66e..c17c6fa 100644 --- a/man/designMatrix.Rd +++ b/man/designMatrix.Rd @@ -20,6 +20,9 @@ designMatrix(object) \item{value}{A design matrix} } +\value{ +A numeric design matrix +} \description{ Extract the design matrix from an object } diff --git a/man/designVariables.Rd b/man/designVariables.Rd index 03bc142..664bf55 100644 --- a/man/designVariables.Rd +++ b/man/designVariables.Rd @@ -12,6 +12,9 @@ designVariables(object) \arguments{ \item{object}{An object, see supported methods below} } +\value{ +A character vector of variable names +} \description{ Extract design variable names from an object } diff --git a/man/dispGroups.Rd b/man/dispGroups.Rd index 6ef770e..e4c1d81 100644 --- a/man/dispGroups.Rd +++ b/man/dispGroups.Rd @@ -12,12 +12,15 @@ dispGroups(object) \arguments{ \item{object}{An object, see supported methods below} } +\value{ +A factor of display group labels +} \description{ Extract displayed group labels from an object } \section{Methods (by class)}{ \itemize{ \item \code{dispGroups(DesignContrast)}: Return the sample groups from a DesignContrast object -, suing display labels +, using display labels }} diff --git a/man/eSetToLongTable.Rd b/man/eSetToLongTable.Rd index bf62490..ad8be35 100644 --- a/man/eSetToLongTable.Rd +++ b/man/eSetToLongTable.Rd @@ -15,13 +15,17 @@ eSetToLongTable( \item{exprsFun}{A function to extract expression values, by default \code{exprs}} -\item{includeOtherAssayData}{Logical, whether other elements in the \code{assayData} environment (if present) should be returned. - -The function extracts exprs (and other values in the \code{assayData} environment), and return it in a long data.frame format with phenotypic data} +\item{includeOtherAssayData}{Logical, whether other elements in the \code{assayData} environment (if present) should be returned.} +} +\value{ +A \code{data.frame} in long format. } \description{ Transform eSet to long data.frame } +\details{ +The function extracts exprs (and other values in the \code{assayData} environment), and return it in a long data.frame format with phenotypic data +} \examples{ data(ribios.ExpressionSet, package="ribiosExpression") exprsLongTbl <- eSetToLongTable(ribios.ExpressionSet) diff --git a/man/fixEmptyColumnName.Rd b/man/fixEmptyColumnName.Rd index 7250a6d..e999234 100644 --- a/man/fixEmptyColumnName.Rd +++ b/man/fixEmptyColumnName.Rd @@ -9,13 +9,17 @@ fixEmptyColumnName(df, prefix = "X") \arguments{ \item{df}{A \code{data.frame}} -\item{prefix}{A character string, the prefix to be used if an column's name is empty. - -If any column has an empty string as name, its replaced by the prefix appended by an index starting from 1} +\item{prefix}{A character string, the prefix to be used if an column's name is empty.} +} +\value{ +A \code{data.frame} with fixed column names. } \description{ Detect if any column has an empty string as name and fix } +\details{ +If any column has an empty string as name, its replaced by the prefix appended by an index starting from 1 +} \examples{ testDf <- data.frame("Col1"=LETTERS[1:3], "Col2"=letters[2:4]) colnames(testDf) <- c("", "") diff --git a/man/groups.Rd b/man/groups.Rd index dc2a8f6..19dcc43 100644 --- a/man/groups.Rd +++ b/man/groups.Rd @@ -12,6 +12,9 @@ groups(object) \arguments{ \item{object}{An object, see supported methods below} } +\value{ +A factor of sample groups +} \description{ Extract sample groups from an object } diff --git a/man/grp2gmt.Rd b/man/grp2gmt.Rd index 554d608..033a8f0 100644 --- a/man/grp2gmt.Rd +++ b/man/grp2gmt.Rd @@ -62,7 +62,7 @@ grpFiles2gmt(c(up.file, down.file), n=-1L, chiptype="HG_U95AV2") } \references{ -See \url{http://www.broadinstitute.org/cmap/index.jsp} for the +See \url{https://www.broadinstitute.org/connectivity-map-cmap} for the use of GRP files in the Connectivity Map web tool. } \author{ diff --git a/man/nContrast.Rd b/man/nContrast.Rd index 4eaa1a6..f9c3271 100644 --- a/man/nContrast.Rd +++ b/man/nContrast.Rd @@ -12,12 +12,15 @@ nContrast(object) \arguments{ \item{object}{An object, see supported methods below} } +\value{ +An integer, number of contrasts +} \description{ Extract the number of contrasts from an object } \section{Methods (by class)}{ \itemize{ -\item \code{nContrast(DesignContrast)}: Return the number of contrast in a DesignContras +\item \code{nContrast(DesignContrast)}: Return the number of contrasts in a DesignContrast object }} diff --git a/man/readEset.Rd b/man/readEset.Rd index 0d1efc8..f6129b4 100644 --- a/man/readEset.Rd +++ b/man/readEset.Rd @@ -27,18 +27,22 @@ readEset( \item{header}{Logical, whether a head line is present} -\item{...}{Passed to \code{\link{readFKtable}} - +\item{...}{Passed to \code{\link{readFKtable}}} +} +\value{ +An \code{ExpressionSet} object. +} +\description{ +Read eSet object from plain files +} +\details{ The function can read in eSet object saved by \code{\link{writeEset}} by parsing three plain text files: \code{exprs.file}, \code{fData.file}, and \code{pData.file}. Currently both \code{tsv} and \code{gct} formats are supported for expression file. -See \code{writeEset} for limitations of these functions.} -} -\description{ -Read eSet object from plain files +See \code{writeEset} for limitations of these functions. } \examples{ data(sample.ExpressionSet, package="Biobase") diff --git a/man/ribiosExpression-package.Rd b/man/ribiosExpression-package.Rd index 855a7eb..c77607a 100644 --- a/man/ribiosExpression-package.Rd +++ b/man/ribiosExpression-package.Rd @@ -6,12 +6,20 @@ \alias{ribiosExpression-package} \title{Data structures and functions for gene expression analysis} \description{ -Data structures and functions for expression analysis. +Provides data structures and utility functions for gene expression analysis. It includes the DesignContrast class for representing study designs and contrasts used in differential expression analysis, functions for importing and exporting expression data in GCT/CLS formats, tools for probeset summarization and filtering, and interfaces to limma-based differential gene expression workflows. The package works with Biobase ExpressionSet objects and integrates with the limma framework. Provides data structures and functions for gene expression analysis +} +\seealso{ +Useful links: +\itemize{ + \item \url{https://github.com/bedapub/ribiosExpression} + \item Report bugs at \url{https://github.com/bedapub/ribiosExpression/issues} +} + } \author{ -\strong{Maintainer}: Jitao David Zhang \email{jitao_david.zhang@roche.com} (\href{https://orcid.org/0000-0002-3085-0909}{ORCID}) [contributor] +\strong{Maintainer}: Jitao David Zhang \email{jitao_david.zhang@roche.com} (\href{https://orcid.org/0000-0002-3085-0909}{ORCID}) } \keyword{internal} diff --git a/man/ribiosExpressionSet.Rd b/man/ribiosExpressionSet.Rd index 9c87965..35b2ff1 100644 --- a/man/ribiosExpressionSet.Rd +++ b/man/ribiosExpressionSet.Rd @@ -4,9 +4,15 @@ \name{ribiosExpressionSet} \alias{ribiosExpressionSet} \title{ribiosExpressionSet: An example of ExpressionSet with artificial expression data} +\format{ +An \code{ExpressionSet} object. +} \description{ ribiosExpressionSet: An example of ExpressionSet with artificial expression data } +\examples{ +data(ribiosExpressionSet) +} \author{ Jitao David Zhang \email{jitao_david.zhang@roche.com} } diff --git a/man/rowscale.ExpressionSet.Rd b/man/rowscale.ExpressionSet.Rd index de1eff5..4a689db 100644 --- a/man/rowscale.ExpressionSet.Rd +++ b/man/rowscale.ExpressionSet.Rd @@ -13,6 +13,9 @@ \item{scale}{Logical, whether the standard deviations of rows should be normalised to one.} } +\value{ +An ExpressionSet object with row-scaled expression values. +} \description{ Perform row-wise scaling to an ExpressionSet object } diff --git a/man/splitPCA.Rd b/man/splitPCA.Rd index a2fbc14..2ff9f5a 100644 --- a/man/splitPCA.Rd +++ b/man/splitPCA.Rd @@ -15,6 +15,9 @@ splitPCA(eset, factor, func = function(e) exprs(e), ...) \item{...}{Passed to \code{pcaScores}} } +\value{ +A \code{data.frame} of PCA scores combined from all splits. +} \description{ Split an eSet object and run PCA on each split, return PCA scores as one data.frame } diff --git a/man/truncateDgeTable.Rd b/man/truncateDgeTable.Rd index 1bc8497..9c5d5e8 100644 --- a/man/truncateDgeTable.Rd +++ b/man/truncateDgeTable.Rd @@ -15,6 +15,3 @@ A list of two elements: 'pos' and 'neg'. Each contains a dgeTable of positively/ \description{ Truncate dgeTable into tables of positively and negatively differentially expressed genes according to the pre-defined criteria } -\references{ -The logic is described at http://rochewiki.roche.com/confluence/display/BIOINFO/Substream+Algorithm -} diff --git a/man/writeGct.Rd b/man/writeGct.Rd index a71ef1b..10d6d36 100644 --- a/man/writeGct.Rd +++ b/man/writeGct.Rd @@ -6,7 +6,7 @@ \alias{writeGct,eSet,ANY,ANY,ANY-method} \alias{writeGct,matrix-method} \alias{writeGct,eSet-method} -\title{Export matrix or eEset that can be coereced as one into gct/cls files} +\title{Export matrix or eSet that can be coerced as one into gct/cls files} \usage{ writeGct(obj, file, feat.name, feat.desc) @@ -23,8 +23,11 @@ writeGct(obj, file, feat.name, feat.desc) \item{feat.desc}{Specifying feature descriptions} } +\value{ +Used for its side effect of writing files; returns invisibly. +} \description{ -Export matrix or eEset that can be coereced as one into gct/cls files +Export matrix or eSet that can be coerced as one into gct/cls files } \section{Methods (by class)}{ \itemize{ diff --git a/man/writeGctCls.Rd b/man/writeGctCls.Rd index b7763e5..274b4bc 100644 --- a/man/writeGctCls.Rd +++ b/man/writeGctCls.Rd @@ -91,7 +91,7 @@ unlink(c(paste(tmpfile, ".cls", sep=""), paste(tmpfile, ".gct", sep=""))) } \references{ -\url{http://www.broadinstitute.org/gsea/doc/GSEAUserGuideTEXT.htm} +\url{https://www.gsea-msigdb.org/gsea/doc/GSEAUserGuideTEXT.htm} } \seealso{ See \code{\link{dfFactor}} for possible values of the diff --git a/man/writeSampleGroups.Rd b/man/writeSampleGroups.Rd index a5d8532..5fc2a46 100644 --- a/man/writeSampleGroups.Rd +++ b/man/writeSampleGroups.Rd @@ -11,13 +11,17 @@ writeSampleGroups(sampleGroups, sampleGroups.file, sampleGroupLevels.file) \item{sampleGroups.file}{Character, file name where the information of sample groups is written to.} -\item{sampleGroupLevels.file}{Character, file name where the information of sample group levels is written to. - -The function is used to export sample group and group level information for differential gene expression analysis.} +\item{sampleGroupLevels.file}{Character, file name where the information of sample group levels is written to.} +} +\value{ +Used for its side effect of writing files. Returns invisibly. } \description{ Write sample groups and group levels into plain text files } +\details{ +The function is used to export sample group and group level information for differential gene expression analysis. +} \examples{ writeSampleGroups(gl(3,4), stdout(), stdout()) }