getReads: Store GenomicRanges of BAM reads in a list

Description Usage Arguments Value

View source: R/utility.r

Description

Store positions of BAM reads in a list of GRanges objects

Usage

1
getReads(samp, chrs, fragsize, ncore)

Arguments

samp

Sample data.frame from readSampleInfo()

chrs

Character vector of chromosome names to select

fragsize

Average fragment length from the sequencing experiment. Reads will be extended up to this size when computing coverage. If set to the value "paired", valid mate pairs for a paired-end sequencing experiment will be loaded instead.

ncore

Number of parallel processes to use

Value

A list of GenomicRanges objects where the ranges represent either extended reads or mate pairs from a BAM file.


jeffbhasin/methylaction documentation built on May 17, 2017, 3:59 p.m.