chakalakka authored on 07/06/2016 09:48:47
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@@ -7,7 +7,7 @@ Author: Aaron Taudt, Maria Colome Tatche, Matthias Heinig, Minh Anh Nguyen |
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Maintainer: Aaron Taudt <aaron.taudt@gmail.com> |
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Description: This package implements functions for combinatorial and differential analysis of ChIP-seq data. It includes uni- and multivariate peak-calling, export to genome browser viewable files, and functions for enrichment analyses. |
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Depends: |
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- R (>= 3.2.0), |
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+ R (>= 3.3.0), |
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GenomicRanges, |
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ggplot2, |
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chromstaRData |
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@@ -49,7 +49,7 @@ |
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#'## Check if the fit is ok |
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#'plot(hmm, type='histogram') |
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#' |
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-callPeaksUnivariate <- function(binned.data, input.data=NULL, prefit.on.chr=NULL, short=TRUE, eps=0.01, init="standard", max.time=NULL, max.iter=5000, num.trials=1, eps.try=NULL, num.threads=1, read.cutoff=TRUE, read.cutoff.quantile=1, read.cutoff.absolute=500, max.mean=Inf, post.cutoff=0.5, control=FALSE, keep.posteriors=FALSE, keep.densities=FALSE, verbosity=1) {
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+callPeaksUnivariate <- function(binned.data, input.data=NULL, prefit.on.chr=NULL, short=TRUE, eps=0.1, init="standard", max.time=NULL, max.iter=5000, num.trials=1, eps.try=NULL, num.threads=1, read.cutoff=TRUE, read.cutoff.quantile=1, read.cutoff.absolute=500, max.mean=Inf, post.cutoff=0.5, control=FALSE, keep.posteriors=FALSE, keep.densities=FALSE, verbosity=1) {
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if (class(binned.data) == 'character') {
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message("Loading file ",binned.data)
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@@ -426,7 +426,7 @@ callPeaksUnivariateAllChr <- function(binned.data, input.data=NULL, eps=0.01, in |
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red.df <- suppressMessages(collapseBins(df, column2collapseBy='state', columns2average=c('score'), columns2drop=c('width',grep('posterior', names(df), value=TRUE), 'counts')))
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red.gr <- GRanges(seqnames=red.df[,1], ranges=IRanges(start=red.df[,2], end=red.df[,3]), strand=red.df[,4], state=red.df[,'state'], score=red.df[,'mean.score']) |
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result$segments <- red.gr |
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- seqlengths(result$segments) <- seqlengths(binned.data) |
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+ seqlengths(result$segments) <- seqlengths(binned.data)[seqlevels(result$segments)] |
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if (!keep.posteriors) {
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result$bins$posteriors <- NULL |
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} |
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@@ -67,7 +67,7 @@ changePostCutoff <- function(model, post.cutoff=0.5, separate.zeroinflation=TRUE |
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red.df <- suppressMessages(collapseBins(df, column2collapseBy='state', columns2average=c('score'), columns2drop=c('width',grep('posteriors', names(df), value=TRUE), 'counts')))
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red.gr <- GRanges(seqnames=red.df[,1], ranges=IRanges(start=red.df[,2], end=red.df[,3]), strand=red.df[,4], state=red.df[,'state'], score=red.df[,'mean.score']) |
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model$segments <- red.gr |
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- seqlengths(model$segments) <- seqlengths(model$bins) |
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+ seqlengths(model$segments) <- seqlengths(model$bins)[seqlevels(model$segments)] |
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stopTimedMessage(ptm) |
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# ## Redo weights |
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# model$weights <- table(model$bins$state) / length(model$bins) |
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#' @param hmm.list A list of models generated by \code{\link{callPeaksUnivariate}}, e.g. 'list(model1,model2,...)'.
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#' @param binary If \code{TRUE}, a matrix of binary instead of decimal states will be returned.
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#' @return Output is a vector of integers representing the combinatorial state of each bin. |
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-#' @seealso \code{link{dec2bin}}, \code{\link{bin2dec}}
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+#' @seealso \code{\link{dec2bin}}, \code{\link{bin2dec}}
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#' @examples |
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#'# Get example BED files for 4 different marks in hypertensive rat (SHR) |
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#'file.path <- system.file("extdata","euratrans", package='chromstaRData')
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#' |
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#' @param hmms A \code{list()} with \code{\link{multiHMM}} objects. Alternatively a character vector with filenames that contain \code{\link{multiHMM}} objects.
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#' @param mode Mode of combination. See \code{\link{Chromstar}} for a description of the \code{mode} parameter.
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-#' @return A \code{link{combinedMultiHMM}} objects with combinatorial states for each condition.
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+#' @return A \code{\link{combinedMultiHMM}} objects with combinatorial states for each condition.
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#' @author Aaron Taudt |
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#' @export |
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#' @examples |
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@@ -253,7 +253,7 @@ combineMultivariates <- function(hmms, mode) {
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segments.cond <- suppressMessages( collapseBins(df, column2collapseBy=cond, columns2drop=c('width', grep('posteriors', names(df), value=TRUE))) )
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segments.cond <- as(segments.cond, 'GRanges') |
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names(mcols(segments.cond)) <- 'combination' |
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- seqlengths(segments.cond) <- seqlengths(bins) |
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+ seqlengths(segments.cond) <- seqlengths(bins)[seqlevels(segments.cond)] |
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segments.separate[[cond]] <- segments.cond |
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} |
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stopTimedMessage(ptm) |
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#' Plotting functions for enrichment analysis of \code{\link{multiHMM}} objects with any annotation of interest, specified as a \code{\link[GenomicRanges]{GRanges}} object.
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#' |
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#' @name enrichment_analysis |
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-#' @return A \code{\link[ggplot2:ggplot]{ggplot}} object containing the plot.
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+#' @return A \code{\link[ggplot2:ggplot]{ggplot}} object containing the plot or a list() with \code{\link[ggplot2:ggplot]{ggplot}} objects if several plots are returned.
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#' @author Aaron Taudt |
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#' @examples |
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#'### Get an example multiHMM ### |
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@@ -239,6 +239,7 @@ bed2GRanges <- function(bedfile, assembly, chromosomes=NULL, remove.duplicate.re |
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} |
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## Select only desired chromosomes |
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+ ptm <- startTimedMessage("Subsetting chromosomes ...")
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data <- data[seqnames(data) %in% chroms2use] |
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data <- keepSeqlevels(data, as.character(unique(seqnames(data)))) |
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## Drop seqlevels where seqlength is NA |
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@@ -248,6 +249,7 @@ bed2GRanges <- function(bedfile, assembly, chromosomes=NULL, remove.duplicate.re |
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if (length(na.seqlevels) > 0) {
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warning("Dropped seqlevels because no length information was available: ", paste0(na.seqlevels, collapse=', '))
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} |
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+ stopTimedMessage(ptm) |
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if (length(data) == 0) {
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stop(paste0('No reads imported!'))
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@@ -18,7 +18,7 @@ multivariateSegmentation <- function(bins, column2collapseBy='state') {
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names(red.df) <- sub('^mean.','', names(red.df))
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segments <- as(red.df, 'GRanges') |
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segments <- keepSeqlevels(segments, seqlevels(bins)) |
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- seqlengths(segments) <- seqlengths(bins) |
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+ seqlengths(segments) <- seqlengths(bins)[seqlevels(segments)] |
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stopTimedMessage(ptm) |
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return(segments) |
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@@ -111,7 +111,7 @@ unis2pseudomulti <- function(uni.hmm.list) {
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red.df <- suppressMessages(collapseBins(df, column2collapseBy='state', columns2drop=c(ind.readcols, ind.widthcol))) |
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red.gr <- GRanges(seqnames=red.df[,1], ranges=IRanges(start=red.df[,2], end=red.df[,3]), strand=red.df[,4], state=red.df[,'state'], combination=red.df[,'combination']) |
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result$segments <- red.gr |
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- seqlengths(result$segments) <- seqlengths(result$bins) |
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+ seqlengths(result$segments) <- seqlengths(result$bins)[seqlevels(result$segments)] |
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## Parameters |
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result$mapping <- mapping |
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# Weights |
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\title{Fit a Hidden Markov Model to a ChIP-seq sample.}
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\usage{
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callPeaksUnivariate(binned.data, input.data = NULL, prefit.on.chr = NULL, |
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- short = TRUE, eps = 0.01, init = "standard", max.time = NULL, |
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+ short = TRUE, eps = 0.1, init = "standard", max.time = NULL, |
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max.iter = 5000, num.trials = 1, eps.try = NULL, num.threads = 1, |
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read.cutoff = TRUE, read.cutoff.quantile = 1, |
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read.cutoff.absolute = 500, max.mean = Inf, post.cutoff = 0.5, |
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@@ -12,7 +12,7 @@ combineMultivariates(hmms, mode) |
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\item{mode}{Mode of combination. See \code{\link{Chromstar}} for a description of the \code{mode} parameter.}
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} |
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\value{
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-A \code{link{combinedMultiHMM}} objects with combinatorial states for each condition.
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+A \code{\link{combinedMultiHMM}} objects with combinatorial states for each condition.
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} |
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\description{
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Combine combinatorial states from several \code{\link{multiHMM}} objects. Combinatorial states can be combined for objects containing multiple marks (\code{mode='mark'}) or multiple conditions (\code{mode='condition'}).
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@@ -34,7 +34,7 @@ plotEnrichment(hmm, annotation, bp.around.annotation = 10000, |
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\item{num.intervals}{Number of intervals for enrichment 'inside' of annotation.}
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} |
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\value{
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-A \code{\link[ggplot2:ggplot]{ggplot}} object containing the plot.
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+A \code{\link[ggplot2:ggplot]{ggplot}} object containing the plot or a list() with \code{\link[ggplot2:ggplot]{ggplot}} objects if several plots are returned.
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A \code{\link[ggplot2]{ggplot}} object (\code{plot=TRUE}) or a named array with fold enrichments (\code{plot=FALSE}).
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} |