NEWS

HTSFilter 1.31.1

-- Remove all references and functionality related to the deprecated DESeq package. -- Vignette has been updated to Rmarkdown from Sweave.

-- Fixed bug for missing parallel option when a CountDataSet is used with HTSFilter

-- Fixed bug in vignette causing error message on dev (related to new estimateDisp function in edgeR package) -- All documentation now automatically done through Roxygen -- Functionality for DESeq pipeline (CountDataSet objects) now deprecated -- Add possibility for parallel computing via BiocParallel -- Recorrect multiple testing correction of p-values in DESeq2 framework (only correct p-values for genes that pass filter) using pAdjustMethod argument in HTSFilter and HTSBasicFilter functions -- Started adding unit testing framework

-- Minor bug fix for integration in edgeR pipeline -- Minor updates in vignette and documentation -- Removed IRanges and GenomicRanges from imports (hard-coded the mcols and colData functions for use in DESeq2 pipeline instead) -- Add BiocStyle to Suggests for vignette style

-- Minor bug fix for integeration in DESeq2 pipeline (which now has automatic independent filtering available) -- HTSFilter now accepts data with multi-factor designs for all input types

-- Updated citation information, minor updates to vignette -- DESeq2, IRanges, and GenomicRanges added to Imports field, and HTSFilter and HTSFilterBasic methods written for objects of with DESeqDataSet signature (from DESeq2 pipeline). Examples illustrating the use of HTSFilter have also been added in the documentation and vignettes. -- DESeq and edgeR moved to Imports field (thanks to Denis Laloë for the suggestion) -- Warning message added when gene ID's are included as a column in the data frame (thanks to Luc Jouneau for the suggestion)

-- Fixed minor bugs in HTSBasicFilter function for rpkm calculation -- Minor changes to vignette

-- Small updates to vignette, fixed small bug in HTSBasicFilter function and doc

-- Vignette updated -- New method HTSBasicFilter for all classes handled by HTSFilter -- Made normalizeData a visible function -- Changes to dependencies (include classes and methods for DESeq, include additional classes for edgeR pipeline: DGEExact, DGEGLM, DGELRT) -- Slight changes/additions to man pages and citation info (paper in revision) -- Inclusion of methods for CountDataSet S4 objects -- Inclusion of methods for additional edgeR objects: DGEList, DGEExact, DGEGLM, and DGELRT now supported -- Minor change in .perConditionSimilarityIndex() to use mean rather than sum (in case of unbalanced experiments)

-- Some additional documentation about the HTSFilter output -- Small changes to vignette: typos, name changed to HTSFilter.pdf to allow calls to vignette("HTSFilter"), added .onAttach function to zzz.R to add HTSFilter vignette to Windows toolbar. -- Added HTSFilter method for signature "data.frame"