makeSegmentCountHistPlots: makeSegmentCountHistPlots
In ge11232002/NGS: Next Generation Sequencing Data Analysis

Description Usage Arguments Details Value Author(s) See Also Examples

Plot the histogram of the number of alignments per read.

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  makeSegmentCountHistPlots(bamFiles,
                            pairedMode = c("paired", "first", "second"),
                            mc.cores = getThreads())

`bamFiles`	The `character`() filenames of input bam files.
`pairedMode`	The `pairedMode` can be "paired", "first", "second". "paired" will load proper pairs; "first" will load all the first reads; "second" will load all mapped mate reads. This argument is ignored when it's single-end read.
`mc.cores`	The number of threads to use. By default, we use a internal function `NGS:::getThreads` to decide.

When it's paired-end reads, the number of alignments is calculated for the whole pair (fragment).

A ggplot object.

Ge Tan

makeFragLengthHistPlot

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  bamfile <- system.file("extdata", "ex1.bam", package="Rsamtools",
                         mustWork=TRUE)
  makeSegmentCountHistPlots(bamfile, pairedMode="paired", mc.cores=1L)