fragSizesDist — fragSizesDist • epiwraps

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)