fragSizesDist: fragSizesDist

In ETHZ-INS/epiwraps: epiwraps: Wrappers for plotting and dealing with epigenomics data

fragSizesDist

Description

fragSizesDist

Usage

fragSizesDist(
  x,
  what = 10000,
  flags = scanBamFlag(isProperPair = TRUE),
  BPPARAM = SerialParam(),
  returnPlot = TRUE
)

Arguments

x	A (named) vector of paths to bam files.
what	Either a positive integer (length 1) indicating how many reads to randomly sample, or a character vector (of length 1) indicating which chromosome to read.
flags	A 'scanBamFlag' object (see ScanBamParam)
BPPARAM	A BiocParallel BPPARAM object for multithreading.
returnPlot	Logical; whether to return a plot.

Value

If 'returnPlot=TRUE', returns a ggplot object, otherwise a data.frame of fragment lengths.

Examples

# example bam file:
bam <- system.file("extdata", "ex1.bam", package="Rsamtools")
fragSizesDist(bam, what=100)

ETHZ-INS/epiwraps documentation built on Dec. 22, 2024, 4:05 a.m.