loadAllData: Function to load all data from a list of bam files

In gerstung-lab/deepSNV: Detection of subclonal SNVs in deep sequencing data.

Function to load all data from a list of bam files

Description

This function uses the parallel package and the bam2R interface to load all nucleotide counts from a list of bam files and a set of regions into a large array.

Usage

loadAllData(files, regions, ..., mc.cores = 1)

Arguments

files	A character vector with the paths to all bam files
regions	Either a GRanges or data.frame with the coordinates of interest
...	Arguments passed to bam2R
mc.cores	Number of cores used for loading, default = 1

Value

counts

Note

Experimental code, subject to changes

Author(s)

mg14

gerstung-lab/deepSNV documentation built on June 3, 2022, 3:05 p.m.