bam2bigwig: bam2bigwig

In ge11232002/NGS: Next Generation Sequencing Data Analysis

Description

Convert a bam file into a bigwig file with coverage.

Usage

  bam2bigwig(bamFiles, bigwigFiles = sub("\\.bam$", ".bw", bamFiles, 
                                         ignore.case = TRUE))

Arguments

bamFiles	The character() filenames of input bam files.
bigwigFiles	The filenames of output bigwig files.

Details

All the mapped reads are loaded, no matter they are paired or not, properly paired or not.

Value

The filenames of output bigwig files.

Author(s)

Ge Tan

Examples

  bamfile <- system.file("extdata", "ex1.bam", package="Rsamtools",
                         mustWork=TRUE)
  bwFile <- tempfile(fileext=".bw")
  bam2bigwig(bamfile, bwFile)
  file.remove(bwFile)

ge11232002/NGS documentation built on May 17, 2019, 12:13 a.m.