loadBroadPeaks: Import broadPeak files into a list of GRanges objects.

Description Usage Arguments Value Author(s)

View source: R/import_data.R

Description

All broadPeak files are assumed to be nested in subdirectories named adter sample names. Based on rtracklayer::import.bed, but adds additional columns present only in broadPeak files.

Usage

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loadBroadPeaks(sample_dir, sample_names,
  peaks_suffix = "_peaks.broadPeak", sub_dir = TRUE)

Arguments

sample_dir

Path to the directory containing the broadPeak files.

sample_names

Vector of sample names.

peaks_suffix

Suffix of the broadPeak files.

sub_dir

If TRUE, count files are nested in subfolders named after sample names, otherwise counts files are directly in sample_dir.

Value

List of GRanges objects corresponding to peak calls from each sample.

Author(s)

Kaur Alasoo


kauralasoo/seqUtils documentation built on May 20, 2019, 7:42 a.m.