importBam {trackViewer}R Documentation

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="+"))
[Package trackViewer version 1.18.3 Index]