fragSizeDist: fragment size distribution

Description Usage Arguments Value Author(s) Examples

View source: R/fragSizeDist.R

Description

estimate the fragment size of bams

Usage

1
2
3
4
5
6
7
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

1
2
3
bamFiles <- dir(system.file("extdata", package="ATACseqQC"), "GL.*.bam$", full.names=TRUE)
bamFiles.labels <- sub(".bam", "", basename(bamFiles))
fragSizeDist(bamFiles, bamFiles.labels)

ATACseqQC documentation built on Nov. 8, 2020, 11 p.m.