SegvisData: SegvisData object and constructors

In welch16/Segvis: Segvis: A package for visualization of high throughput sequencing data along genomic segments

Description

SegvisData is a subclass of GenomicRanges, used to visualize high-thoughput sequencing experiments across a set of user - defined genomic regions.

Usage

SegvisData(regions, files, is_pet = rep(FALSE, length(files)), frag_len = 1,
  mc.cores = getOption("mc.cores", 2L))

Arguments

regions	a GRanges object with the regions to be considered.
files	a character vector with the location of the bam files that contain the aligned reads.
is_pet	a logical vector with the same length as files indicating if the aligned reads in the respective bam file are paired.
frag_len	a numeric vector representing the average fragment length to which the aligned reads in their respective bam file are going to be extended. For PE reads, this parameter is not considered.
mc.cores	a numeric value with the number of cores to use, i.e. at most how many child processes will be run simultaneously.

Value

SegvisData returns a SegvisData object which contains the forward, backward and aggregated coverage for every aligned read file in files.

welch16/Segvis documentation built on May 4, 2019, 4:18 a.m.