fragSizeDist: fragment size distribution
In jianhong/ATACseqQC: ATAC-seq Quality Control

fragSizeDist

R Documentation

fragment size distribution

Description

estimate the fragment size of bams

Usage

fragSizeDist(
  bamFiles,
  bamFiles.labels,
  index = bamFiles,
  ylim = NULL,
  logYlim = NULL
)

Arguments

`bamFiles`	A vector of characters indicates the file names of bams.
`bamFiles.labels`	labels of the bam files, used for pdf file naming.
`index`	The names of the index file of the 'BAM' file being processed; This is given without the '.bai' extension.
`ylim`	numeric(2). ylim of the histogram.
`logYlim`	numeric(2). ylim of log-transformed histogram for the insert.

Value

Invisible fragment length distribution list.

Author(s)

Jianhong Ou

Examples

bamFiles <- dir(system.file("extdata", package="ATACseqQC"), "GL.*.bam$", full.names=TRUE)
bamFiles.labels <- sub(".bam", "", basename(bamFiles))
fragSizeDist(bamFiles, bamFiles.labels)

jianhong/ATACseqQC documentation built on June 14, 2025, 1:23 a.m.