variableWidthBins: Make variable-width bins

In chromstaR: Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

Description

Make variable-width bins based on a reference BAM file. This can be a simulated file (produced by TODO: insert link and aligned with your favourite aligner) or a real reference.

Usage

variableWidthBins(reads, binsizes, chromosomes = NULL)

Arguments

reads	A GRanges-class with reads. See readBamFileAsGRanges and readBedFileAsGRanges.
binsizes	A vector with binsizes. Resulting bins will be close to the specified binsizes.
chromosomes	A subset of chromosomes for which the bins are generated.

Details

Variable-width bins are produced by first binning the reference BAM file with fixed-width bins and selecting the desired number of reads per bin as the (non-zero) maximum of the histogram. A new set of bins is then generated such that every bin contains the desired number of reads.

Value

A list() of GRanges-class objects with variable-width bins.

Author(s)

Aaron Taudt

Examples

## Get an example BAM file with ChIP-seq reads
bamfile <- system.file("extdata", "euratrans", "lv-H3K4me3-BN-female-bio1-tech1.bam",
                      package="chromstaRData")
## Read the file into a GRanges object
reads <- readBamFileAsGRanges(bamfile, chromosomes='chr12', pairedEndReads=FALSE,
                    min.mapq=10, remove.duplicate.reads=TRUE)
## Make variable-width bins of size 1000bp
bins <- variableWidthBins(reads, binsizes=1000)
## Plot the distribution of binsizes
hist(width(bins[['1000']]), breaks=50)

chromstaR documentation built on Nov. 8, 2020, 8:29 p.m.