importBam: Reading data from a BAM file

In jianhong/trackViewer: A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data

Reading data from a BAM file

Description

Read a track object from a BAM file

Usage

importBam(file, file2, ranges = GRanges(), pairs = FALSE)

Arguments

file	The path to the BAM file to read.
file2	The path to the second BAM file to read.
ranges	An object of GRanges to indicate the range to be imported
pairs	logical object to indicate the BAM is paired or not. See readGAlignments

Value

a track object

See Also

See Also as importScore, track, viewTracks

Examples

bamfile <- system.file("extdata", "ex1.bam", package="Rsamtools",
mustWork=TRUE)
dat <- importBam(file=bamfile, ranges=GRanges("seq1", IRanges(1, 50), strand="+"))

jianhong/trackViewer documentation built on March 17, 2024, 2:16 p.m.