crossLinkR: Wrapper function for CrossLinkR package

In daewoooo/CrossLinkR: R package to search for crosslinks in Hi-C data

Description

Wrapper function for CrossLinkR package

Usage

crossLinkR(bamFile, vcfFile, outputfolder = "./CrossLinkR_analysis",
  yieldSize = 1e+05, readLen = 100, min.mapq = 10, min.baseq = 20,
  nCPU = 3, blacklist = NULL)

Arguments

bamFile	Bamfile with paired-end reads sorted by readName.
vcfFile	VCF file containing phased alleles
outputfolder	Output directory. If non-existent it will be created.
yieldSize	Number of reads to be loaded as a chunk to save memory (Default: 1000000)
readLen	Length of the read in bp.
min.mapq	Minimum mapping quality of any given read.
min.baseq	Minimum base quality to consider SNV for crosslink.
nCPU	The number of CPUs to use. Should not be more than available on your machine.
blacklist	List of regions to be excluded from the analysis (format: chromosome start end)

Author(s)

David Porubsky

daewoooo/CrossLinkR documentation built on March 7, 2020, 10:34 p.m.