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)

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