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commit 70bdf8f2f457b091c3b0c74bc94aadc6c292a00e Author: Andreas Tille <[email protected]> Date: Mon Oct 2 22:21:18 2017 +0200 Adapt patches --- debian/patches/remove-locfit | 127 +++++++++++++++---------------------------- 1 file changed, 43 insertions(+), 84 deletions(-) diff --git a/debian/patches/remove-locfit b/debian/patches/remove-locfit index e796487..649642d 100644 --- a/debian/patches/remove-locfit +++ b/debian/patches/remove-locfit @@ -2,7 +2,7 @@ Author: Michael R. Crusoe <[email protected]> Description: r-cran-locfit is non-free and not yet packaged for Debian --- a/R/core.R +++ b/R/core.R -@@ -153,7 +153,7 @@ NULL +@@ -156,7 +156,7 @@ NULL #' Wald significance tests (defined by \code{\link{nbinomWaldTest}}), #' or the likelihood ratio test on the difference in deviance between a #' full and reduced model formula (defined by \code{\link{nbinomLRT}}) @@ -11,7 +11,7 @@ Description: r-cran-locfit is non-free and not yet packaged for Debian #' for the type of fitting of dispersions to the mean intensity. #' See \code{\link{estimateDispersions}} for description. #' @param betaPrior whether or not to put a zero-mean normal prior on -@@ -202,7 +202,6 @@ NULL +@@ -206,7 +206,6 @@ NULL #' Michael I Love, Wolfgang Huber, Simon Anders: Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 2014, 15:550. \url{http://dx.doi.org/10.1186/s13059-014-0550-8} #' @import BiocGenerics BiocParallel S4Vectors IRanges GenomicRanges SummarizedExperiment Biobase Rcpp methods #' @@ -19,7 +19,7 @@ Description: r-cran-locfit is non-free and not yet packaged for Debian #' @importFrom genefilter rowVars filtered_p #' @importFrom Hmisc wtd.quantile #' -@@ -234,14 +233,14 @@ NULL +@@ -242,14 +241,14 @@ NULL #' #' @export DESeq <- function(object, test=c("Wald","LRT"), @@ -36,7 +36,7 @@ Description: r-cran-locfit is non-free and not yet packaged for Debian stopifnot(is.logical(quiet)) stopifnot(is.numeric(minReplicatesForReplace)) stopifnot(is.logical(parallel)) -@@ -495,7 +494,7 @@ estimateSizeFactorsForMatrix <- function +@@ -507,7 +506,7 @@ estimateSizeFactorsForMatrix <- function #' examples below. #' #' @param object a DESeqDataSet @@ -45,7 +45,7 @@ Description: r-cran-locfit is non-free and not yet packaged for Debian #' for the type of fitting of dispersions to the mean intensity. #' See \code{\link{estimateDispersions}} for description. #' @param outlierSD the number of standard deviations of log -@@ -694,7 +693,7 @@ estimateDispersionsGeneEst <- function(o +@@ -721,7 +720,7 @@ estimateDispersionsGeneEst <- function(o #' @rdname estimateDispersionsGeneEst #' @export @@ -54,7 +54,7 @@ Description: r-cran-locfit is non-free and not yet packaged for Debian minDisp=1e-8, quiet=FALSE) { if (is.null(mcols(object)$allZero)) { -@@ -711,7 +710,7 @@ estimateDispersionsFit <- function(objec +@@ -738,7 +737,7 @@ estimateDispersionsFit <- function(objec ...then continue with testing using nbinomWaldTest or nbinomLRT") } @@ -63,7 +63,7 @@ Description: r-cran-locfit is non-free and not yet packaged for Debian stopifnot(length(fitType)==1) stopifnot(length(minDisp)==1) if (fitType == "parametric") { -@@ -725,18 +724,18 @@ estimateDispersionsFit <- function(objec +@@ -752,18 +751,18 @@ estimateDispersionsFit <- function(objec fitType <- "local" } } @@ -88,7 +88,7 @@ Description: r-cran-locfit is non-free and not yet packaged for Debian stop("unknown fitType") } -@@ -1849,16 +1848,17 @@ parametricDispersionFit <- function( mea +@@ -1838,16 +1837,17 @@ parametricDispersionFit <- function( mea # Local fit of dispersion to the mean intensity # fitting is done on log dispersion, log mean scale @@ -118,7 +118,7 @@ Description: r-cran-locfit is non-free and not yet packaged for Debian # convenience function for testing the log likelihood --- a/R/methods.R +++ b/R/methods.R -@@ -493,7 +493,7 @@ estimateSizeFactors.DESeqDataSet <- func +@@ -506,7 +506,7 @@ estimateSizeFactors.DESeqDataSet <- func setMethod("estimateSizeFactors", signature(object="DESeqDataSet"), estimateSizeFactors.DESeqDataSet) @@ -127,7 +127,7 @@ Description: r-cran-locfit is non-free and not yet packaged for Debian maxit=100, quiet=FALSE, modelMatrix=NULL) { # Temporary hack for backward compatibility with "old" DESeqDataSet # objects. Remove once all serialized DESeqDataSet objects around have -@@ -522,7 +522,7 @@ this column could have come in during co +@@ -535,7 +535,7 @@ this column could have come in during co mcols(object) <- mcols(object)[,!(mcols(mcols(object))$type %in% c("intermediate","results")),drop=FALSE] } stopifnot(length(maxit)==1) @@ -136,7 +136,7 @@ Description: r-cran-locfit is non-free and not yet packaged for Debian noReps <- checkForExperimentalReplicates(object, modelMatrix) if (noReps) { -@@ -615,7 +615,7 @@ checkForExperimentalReplicates <- functi +@@ -628,7 +628,7 @@ checkForExperimentalReplicates <- functi #' @rdname estimateDispersions #' @aliases estimateDispersions estimateDispersions,DESeqDataSet-method #' @param object a DESeqDataSet @@ -145,7 +145,7 @@ Description: r-cran-locfit is non-free and not yet packaged for Debian #' for the type of fitting of dispersions to the mean intensity. #' \itemize{ #' \item parametric - fit a dispersion-mean relation of the form: -@@ -623,10 +623,6 @@ checkForExperimentalReplicates <- functi +@@ -636,10 +636,6 @@ checkForExperimentalReplicates <- functi #' via a robust gamma-family GLM. The coefficients \code{asymptDisp} and \code{extraPois} #' are given in the attribute \code{coefficients} of the \code{\link{dispersionFunction}} #' of the object. @@ -180,47 +180,6 @@ Description: r-cran-locfit is non-free and not yet packaged for Debian } } ---- a/inst/doc/DESeq2.Rnw -+++ b/inst/doc/DESeq2.Rnw -@@ -961,9 +961,7 @@ Above, we used a parametric fit for the - closed-form expression for the variance stabilizing transformation is - used by \Rfunction{varianceStabilizingTransformation}, which is - derived in the file \texttt{vst.pdf}, that is distributed in the --package alongside this vignette. If a local fit is used (option --\Robject{fitType="locfit"} to \Rfunction{estimateDispersions}) a --numerical integration is used instead. -+package alongside this vignette. - - <<vsd1, echo=FALSE, fig.width=4.5, fig.height=4.5, fig.show="asis", fig.small=TRUE, fig.pos="!bt", fig.cap="VST and log2. Graphs of the variance stabilizing transformation for sample 1, in blue, and of the transformation $f(n) = \\log_2(n/s_1)$, in black. $n$ are the counts and $s_1$ is the size factor for the first sample.\\label{figure/vsd1-1}">>= - px <- counts(dds)[,1] / sizeFactors(dds)[1] ---- a/tests/testthat/test_disp_fit.R -+++ b/tests/testthat/test_disp_fit.R -@@ -78,7 +78,7 @@ expect_equal(dispD2DESeq, dispD2Num, tol - # test fit alternative - dds <- makeExampleDESeqDataSet() - dds <- estimateSizeFactors(dds) --ddsLocal <- estimateDispersions(dds, fitType="local") -+#ddsLocal <- estimateDispersions(dds, fitType="local") - ddsMean <- estimateDispersions(dds, fitType="mean") - ddsMed <- estimateDispersionsGeneEst(dds) - useForMedian <- mcols(ddsMed)$dispGeneEst > 1e-7 ---- a/tests/testthat/test_vst.R -+++ b/tests/testthat/test_vst.R -@@ -4,7 +4,7 @@ dds <- estimateSizeFactors(dds) - dds <- estimateDispersionsGeneEst(dds) - dds <- estimateDispersionsFit(dds, fitType="parametric") - vsd <- varianceStabilizingTransformation(dds, blind=FALSE) --dds <- estimateDispersionsFit(dds, fitType="local") -+#dds <- estimateDispersionsFit(dds, fitType="local") - vsd <- varianceStabilizingTransformation(dds, blind=FALSE) - dds <- estimateDispersionsFit(dds, fitType="mean") - vsd <- varianceStabilizingTransformation(dds, blind=FALSE) -@@ -28,4 +28,4 @@ vsd <- vst(counts(dds)) - dds <- makeExampleDESeqDataSet(n=100, m=10, betaSD=1.5) - nf <- matrix(exp(rnorm(1000,0,.2)),ncol=10) - normalizationFactors(dds) <- nf --vsd <- varianceStabilizingTransformation(dds, fitType="local") -+#vsd <- varianceStabilizingTransformation(dds, fitType="local") --- a/DESCRIPTION +++ b/DESCRIPTION @@ -12,7 +12,7 @@ Description: Estimate variance-mean depe @@ -231,10 +190,10 @@ Description: r-cran-locfit is non-free and not yet packaged for Debian + methods, geneplotter, ggplot2, Hmisc, Rcpp (>= 0.11.0) Depends: S4Vectors (>= 0.9.25), IRanges, GenomicRanges, SummarizedExperiment (>= 1.1.6) - Suggests: testthat, knitr, BiocStyle, vsn, pheatmap, RColorBrewer, + Suggests: testthat, knitr, BiocStyle, vsn, pheatmap, RColorBrewer, IHW, --- a/NAMESPACE +++ b/NAMESPACE -@@ -86,7 +86,6 @@ importFrom(graphics,axis) +@@ -88,7 +88,6 @@ importFrom(graphics,axis) importFrom(graphics,hist) importFrom(graphics,plot) importFrom(graphics,points) @@ -242,32 +201,32 @@ Description: r-cran-locfit is non-free and not yet packaged for Debian importFrom(stats,Gamma) importFrom(stats,as.formula) importFrom(stats,coef) ---- a/vignettes/DESeq2.Rnw -+++ b/vignettes/DESeq2.Rnw -@@ -961,9 +961,7 @@ Above, we used a parametric fit for the - closed-form expression for the variance stabilizing transformation is - used by \Rfunction{varianceStabilizingTransformation}, which is - derived in the file \texttt{vst.pdf}, that is distributed in the --package alongside this vignette. If a local fit is used (option --\Robject{fitType="locfit"} to \Rfunction{estimateDispersions}) a --numerical integration is used instead. -+package alongside this vignette. - - <<vsd1, echo=FALSE, fig.width=4.5, fig.height=4.5, fig.show="asis", fig.small=TRUE, fig.pos="!bt", fig.cap="VST and log2. Graphs of the variance stabilizing transformation for sample 1, in blue, and of the transformation $f(n) = \\log_2(n/s_1)$, in black. $n$ are the counts and $s_1$ is the size factor for the first sample.\\label{figure/vsd1-1}">>= - px <- counts(dds)[,1] / sizeFactors(dds)[1] -@@ -1450,15 +1448,6 @@ and the variability of the gene-wise est - plotDispEsts(dds) - @ - --\subsubsection{Local or mean dispersion fit} -- --A local smoothed dispersion fit is automatically substitited in the case that --the parametric curve doesn't fit the observed dispersion mean relationship. --This can be prespecified by providing the argument --\Robject{fitType="local"} to either \Rfunction{DESeq} or \Rfunction{estimateDispersions}. --Additionally, using the mean of gene-wise disperion estimates as the --fitted value can be specified by providing the argument \Robject{fitType="mean"}. -- - \subsubsection{Supply a custom dispersion fit} - - Any fitted values can be provided during dispersion estimation, using +--- a/tests/testthat/test_disp_fit.R ++++ b/tests/testthat/test_disp_fit.R +@@ -78,7 +78,7 @@ test_that("the fitting of dispersion giv + # test fit alternative + dds <- makeExampleDESeqDataSet() + dds <- estimateSizeFactors(dds) +- ddsLocal <- estimateDispersions(dds, fitType="local") ++# ddsLocal <- estimateDispersions(dds, fitType="local") + ddsMean <- estimateDispersions(dds, fitType="mean") + ddsMed <- estimateDispersionsGeneEst(dds) + useForMedian <- mcols(ddsMed)$dispGeneEst > 1e-7 +--- a/tests/testthat/test_vst.R ++++ b/tests/testthat/test_vst.R +@@ -6,7 +6,7 @@ test_that("vst works", { + dds <- estimateDispersionsGeneEst(dds) + dds <- estimateDispersionsFit(dds, fitType="parametric") + vsd <- varianceStabilizingTransformation(dds, blind=FALSE) +- dds <- estimateDispersionsFit(dds, fitType="local") ++# dds <- estimateDispersionsFit(dds, fitType="local") + vsd <- varianceStabilizingTransformation(dds, blind=FALSE) + dds <- estimateDispersionsFit(dds, fitType="mean") + vsd <- varianceStabilizingTransformation(dds, blind=FALSE) +@@ -30,5 +30,5 @@ test_that("vst works", { + dds <- makeExampleDESeqDataSet(n=100, m=10, betaSD=1.5) + nf <- matrix(exp(rnorm(1000,0,.2)),ncol=10) + normalizationFactors(dds) <- nf +- vsd <- varianceStabilizingTransformation(dds, fitType="local") ++# vsd <- varianceStabilizingTransformation(dds, fitType="local") + }) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-deseq2.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
