read_bam_file {segmenter}R Documentation

Read bam files

Description

Count the reads in each range of the GRanges object

Usage

read_bam_file(file, features, ...)

Arguments

file

A string. The path to the file.

features

A GRanges object.

...

Other arguments passed to bamCount.

Value

A matrix

Examples

# locate the bam file
bam_file <- system.file("extdata", "randomBam.bam", package = "bamsignals")

# load a granges object
rand_anno <- system.file("extdata",
                         "randomAnnot.Rdata",
                         package = "bamsignals")
features <- GenomicRanges::promoters(get(load(rand_anno)))

# count reads in ranges
read_bam_file(bam_file, features)


[Package segmenter version 0.99.14 Index]