Prepare package for Bioconductor submission

.Rbuildignore

@@ -7,3 +7,5 @@
 ^Makefile$
 ^coverage\.txt$
 ^coverage\.r$
+^\.github$
+^NEWS$

DESCRIPTION

@@ -1,16 +1,21 @@
 Package: ribiosExpression
 Type: Package
-Title: Expression Analysis with RibiosExpression
+Title: Data Structures and Utilities for Gene Expression Analysis
 Version: 1.3.5
-Date: 2025-01-30
 Authors@R:
   person(given = "Jitao David",
          family = "Zhang",
-         role = c("aut", "cre", "ctb"),
+         role = c("aut", "cre"),
          email = "jitao_david.zhang@roche.com",
          comment = c(ORCID="0000-0002-3085-0909"))
-Description: Data structures and functions for expression analysis.
-Depends: R (>= 3.5.0)
+Description: 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.
+Depends: R (>= 4.4.0)
 Imports:
     methods,
     stats,
@@ -28,9 +33,17 @@ Imports:
     openxlsx
 Suggests:
     testthat,
-    grid
+    grid,
+    BiocStyle,
+    knitr,
+    rmarkdown
 License: GPL-3
 Encoding: UTF-8
+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
 Collate: 
     'AllClasses.R'

NEWS.md

@@ -0,0 +1,175 @@
+# Changes in ribiosExpression
+
+## Changes in version 1.3.5
+
+### Bioconductor preparation
+- Added `biocViews` to DESCRIPTION.
+- Added BiocStyle vignette.
+- Updated R dependency to >= 4.4.0.
+- Added `@return` tags to all exported functions.
+- Fixed typos in documentation.
+- Replaced `class(x) %in%` with `is.numeric()`.
+- Converted NEWS to NEWS.md format.
+
+## Changes in version 1.0-39
+
+- `parseDesignContrast` adds new parameter `expSampleNames` to allow sample
+  name consistency check with input matrix.
+
+## Changes in version 1.0-34
+
+- `DesignContrast` prints error message if validity is violated.
+- `parseDesignContrastFile` fixes a mistake of assigning group levels.
+- `parseDesignContrastFile` now accepts the `dispLevelStr` option.
+
+## Changes in version 1.0-33
+
+- `parseDesignContrastStr` fixes two errors.
+
+## Changes in version 1.0-32
+
+- Add `DesignContrast` object.
+
+## Changes in version 1.0-29
+
+- Add new functionality in keepMaxMeanProbes.Rscript: able to read from .CHIP
+  file.
+- keepMaxMeanProbes.Rscript now does not depend on the S4 class ExpressionSet
+  anymore, therefore much faster.
+
+## Changes in version 1.0-28
+
+- Debug keepMaxMeanProbes.Rscript: `extname` returns NA if not found, therefore
+  an additional check is added.
+
+## Changes in version 1.0-27
+
+- Function extension in `ChipFetcher2ExpressionSet`: now non-Affymetrix
+  probesets are supported as well.
+
+## Changes in version 1.0-26
+
+- The main body of `readCls` has been moved to `ribiosIO::read_cls`. `readCls`
+  becomes a synonym for compatibility.
+
+## Changes in version 1.0-25
+
+- Improvement in `readCls`: error messages provide more informative details for
+  mal-formatted files.
+
+## Changes in version 1.0-24
+
+- Bug fix in `writeEset`: expression matrix is written without quotes.
+- New script: keepMaxMeanProbes.Rscript filters duplicated genes by taking the
+  one with maximum average expression.
+
+## Changes in version 1.0-23
+
+- Bug fix in `readGct`: if input feature names have duplicates, the exprs
+  matrix row names are changed.
+
+## Changes in version 1.0-22
+
+- Move exprsMat2gct.Rscript to the ribiosIO package.
+- `writeGct` has been refactored for matrix in ribiosIO, and re-implemented as
+  an S4-method for matrix and ExpressionSet.
+
+## Changes in version 1.0-21
+
+- Add exprsMat2gct.Rscript to convert between expression matrix files and GCT
+  files.
+
+## Changes in version 1.0-20
+
+- `ChipFetcher2ExpressionSet`: add option orthologue.
+- `keepMaxStatProbe` uses `function(x) mean(x, na.rm=TRUE)` as default
+  function.
+
+## Changes in version 1.0-19
+
+- limma2gsea.Rscript is updated.
+
+## Changes in version 1.0-18
+
+- Refactor GSEA-related functions that are not dependent on the Biobase data
+  structure to the ribiosGSEA package.
+
+## Changes in version 1.0-17
+
+- limma2gsea.Rscript guarantees no replicated gene symbols after orthologue
+  mapping.
+
+## Changes in version 1.0-16
+
+- Add limma2gsea.Rscript to inst/Rscript.
+
+## Changes in version 1.0-15
+
+- The ribiosAnnotation package has been removed from the dependency list.
+- Add comp_diff.Rscript to inst/Rscript.
+
+## Changes in version 1.0-14
+
+- The deprecation message of `remainHighestVarProbe` and `keepHighestVarProbe`
+  have been updated.
+
+## Changes in version 1.0-13
+
+- The `rowscale` method warns if the input ExpressionSet does not have
+  'lockedEnvironment' as storageMode.
+
+## Changes in version 1.0-12
+
+- Low-level functions for computational drug repositioning refactored into
+  ribiosReposition.
+
+## Changes in version 1.0-11
+
+- Add feature in `summarizeProbesets`: option `keep.featureNames`.
+- Rename and rewrite `sprintGmt` to `formatGmt` as S4 method.
+
+## Changes in version 1.0-10
+
+- Bugfix in `readEset` for numeric column names.
+- Add `annotate` and `reannotate` methods.
+- Add documentation for the `ribios.ExpressionSet` object.
+
+## Changes in version 1.0-9
+
+- Add `kendallW` function and `kendallWmat` S4-method.
+
+## Changes in version 1.0-8
+
+- PCA-related data structures and functions are refactored into the ribiosPCA
+  package.
+
+## Changes in version 1.0-7
+
+- Add `summarizeProbesets` to summarize probesets.
+- NAMESPACE are now explicitly stated.
+
+## Changes in version 1.0-6
+
+- Add dependency on the ribiosAnnotation package.
+- Add `writeEset` and `readEset` functions.
+- `readFKdata` was renamed as `readFKtable`.
+
+## Changes in version 1.0-5
+
+- Add git version control.
+
+## Changes in version 1.0-4
+
+- Move data.frame and matrix functions to the ribiosUtils package.
+
+## Changes in version 1.0-3
+
+- Refactor `read_gct` into ribiosIO for efficiency.
+
+## Changes in version 1.0-2
+
+- Change `keepHighestVarProbe` to more generalized `keepMaxStatProbe`.
+
+## Changes in version 1.0-1
+
+- Remove the path option from the `readGctCls` function.

R/AllGenerics.R

@@ -16,12 +16,14 @@ setGeneric("exprsToLong", function(x,...) standardGeneric("exprsToLong"))
 
 #' Extract contrastNames from an object
 #' @param object An object, see supported methods below
+#' @return A character vector of contrast names
 #' @aliases contrastNames,DesignContrast-method
 #' @exportMethod contrastNames
 setGeneric("contrastNames", function(object) standardGeneric("contrastNames"))
 
 #' Extract design variable names from an object
 #' @param object An object, see supported methods below
+#' @return A character vector of variable names
 #' @aliases designVariables,DesignContrast-method
 #' @exportMethod designVariables
 setGeneric("designVariables", function(object)
@@ -30,20 +32,23 @@ setGeneric("designVariables", function(object)
 #' Extract sample groups from an object
 #'
 #' @param object An object, see supported methods below
+#' @return A factor of sample groups
 #' @exportMethod groups
 #' @aliases groups,DesignContrast-method
 setGeneric("groups", function(object) standardGeneric("groups"))
 
 #' Extract displayed group labels from an object
 #'
 #' @param object An object, see supported methods below
+#' @return A factor of display group labels
 #' @exportMethod dispGroups
 #' @aliases dispGroups,DesignContrast-method
 setGeneric("dispGroups", function(object) standardGeneric("dispGroups"))
 
 #' Extract the design matrix from an object
 #'
 #' @param object An object, see supported methods below
+#' @return A numeric design matrix
 #' @exportMethod designMatrix
 #' @aliases designMatrix,DesignContrast-method
 setGeneric("designMatrix", function(object) standardGeneric("designMatrix"))
@@ -52,13 +57,14 @@ setGeneric("designMatrix", function(object) standardGeneric("designMatrix"))
 #'
 #' @param object An object, see supported methods below
 #' @param value Design matrix
-#' @exportMethod `designMatrix<-`
+#' @return The modified object
 setGeneric("designMatrix<-", function(object, value) standardGeneric("designMatrix<-"))
 
 
 #' Extract the contrast matrix from an object
 #'
 #' @param object An object, see supported methods below
+#' @return A numeric contrast matrix
 #' @exportMethod contrastMatrix
 #' @aliases contrastMatrix,DesignContrast-method
 setGeneric("contrastMatrix", function(object) standardGeneric("contrastMatrix"))
@@ -67,29 +73,31 @@ setGeneric("contrastMatrix", function(object) standardGeneric("contrastMatrix"))
 #'
 #' @param object An object, see supported methods below
 #' @param value Contrast matrix
-#' @exportMethod `contrastMatrix<-`
+#' @return The modified object
 setGeneric("contrastMatrix<-", function(object, value) standardGeneric("contrastMatrix<-"))
 
 
 #' Extract the contrast annotation data.frame from an object
 #'
 #' @param object An object, see supported methods below
+#' @return A data.frame annotating contrasts
 #' @exportMethod contrastAnnotation
 #' @aliases contrastAnnotation,DesignContrast-method
 setGeneric("contrastAnnotation", function(object) standardGeneric("contrastAnnotation"))
 
-#' Assign contrast annotaiton to an object
+#' Assign contrast annotation to an object
 #'
 #' @param object An object, see supported methods below
-#' @param value Contrast anaotation data.frame
-#' @exportMethod `contrastAnnotation<-`
+#' @param value Contrast annotation data.frame
+#' @return The modified object
 setGeneric("contrastAnnotation<-", function(object, value)
   standardGeneric("contrastAnnotation<-"))
 
 
 #' Extract the number of contrasts from an object
 #'
 #' @param object An object, see supported methods below
+#' @return An integer, number of contrasts
 #' @aliases nContrast,DesignContrast-method
 #' @exportMethod nContrast
 setGeneric("nContrast", function(object) standardGeneric("nContrast"))
@@ -240,12 +248,13 @@ setGeneric("annotate",
 setGeneric("reannotate",
            function(object, check.target,...) standardGeneric("reannotate"))
 
-#' 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
 #' @keywords methods
 #' @param obj The input object, see methods below for supported data types
 #' @param file The output file
 #' @param feat.name Specifying feature names
 #' @param feat.desc Specifying feature descriptions
+#' @return Used for its side effect of writing files; returns invisibly.
 #' @aliases writeGct,matrix,ANY,ANY,ANY-method writeGct,eSet,ANY,ANY,ANY-method
 #' @exportMethod writeGct
 setGeneric("writeGct", function(obj, file, feat.name, feat.desc)

R/AllMethods.R

@@ -12,7 +12,7 @@ return(object@groups)
 })
 
 #' @describeIn dispGroups Return the sample groups from a DesignContrast object
-#'     , suing display labels
+#'     , using display labels
 #' @export
 setMethod("dispGroups", "DesignContrast", function(object) {
   groups <- object@groups
@@ -68,7 +68,7 @@ setReplaceMethod("contrastAnnotation", "DesignContrast", function(object, value)
   return(object)
 })
 
-#' @describeIn nContrast Return the number of contrast in a DesignContras
+#' @describeIn nContrast Return the number of contrasts in a DesignContrast
 #'     object
 #' @export
 setMethod("nContrast", "DesignContrast", function(object) {
@@ -96,7 +96,7 @@ setMethod("exprsToLong", "matrix", function(x, idvar="illID",timevar="hybridID",
                                             ids=rownames(x), valueType="raw") {
   x <- as.data.frame(x)
   colnames(x) <- paste(valuevar, colnames(x), sep=".")
-  va <- 1:ncol(x)
+  va <- seq_len(ncol(x))
   x[,idvar] <- ids
   xLong <- reshape(x, idvar=idvar, varying=va, timevar=timevar, direction="long")
   rownames(xLong) <- NULL
@@ -115,6 +115,7 @@ setMethod("exprsToLong", "eSet", function(x) {
 #' @param x An ExpressionSet object.
 #' @param center Logical, whether the mean values of rows should be set to zero.
 #' @param scale Logical, whether the standard deviations of rows should be normalised to one.
+#' @return An ExpressionSet object with row-scaled expression values.
 #' 
 #' @importFrom ribiosUtils rowscale
 #' @export
@@ -190,7 +191,7 @@ setMethod("formatGmt",
             if(length(comment)==1)
               comment <- rep(comment, length(title))
             stopifnot(identical(length(title), length(comment)))
-            sapply(1:length(genes),
+            sapply(seq_along(genes),
                    function(x) formatGmt(title[x], comment[x], genes[[x]])
             )
           })