limacc: LiMACC algorithm

In wbaopaul/limacc: LiMACC

Description

Identify significant chromatin interations for multiple chromosome conformation capture assays

Usage

limacc(fragment_file, contact_file, dtype = "CHiC",
  peakFile4HiChIP = NULL, out_filename = "sigRes.txt",
  comb_rep = "merge", numG = 100, hcrc = 0.9, fdr = 0.1,
  nIter = 20, maxN = 10000, minLen = NULL, maxLen = NULL,
  minDist = 1000, maxDist = 2 * 10^6, adj.method = "IHW",
  adj.sdepth = NULL, updateMethod = "smooth")

Arguments

fragment_file	the name of restriction enzyme file for CHiC/CC or binned fragment_file for HiChIP
contact_file	contact map file(s)
dtype	data type, CHiC/CC/HiChIP
peakFile4HiChIP	file of coordinate of 1D peak (bed file or similar format) for HiChIP, NULL for other type of data
out_filename	output file name
comb_rep	if length(contact_file)>1, merge or pool replicates (default merge for CHiC; pool for HiChIP)
numG	number of groups for limacc (default 100)
hcrc	initial guess of backgound proportion (default 0.9)
fdr	fdr cutoff used for the final output (default 0.05)
nIter	maxmimum number of iterations (default 20)
maxN	filter contacts that wiht more than maxN counts (default 10000)
minLen	filter otherEnd fragments with length smaller than minLen
maxLen	filter otherEnd fragments with length greater than maxLen
minDist	minimum distance in bp, default 1000bp
maxDist	maximum distance in bp, default 2Mb
adj.method	method for adjusting p-value (default 'IHW')
adj.sdepth	the number (in million) to which the sequence depth should be normalized, default NULL means do not adjust the total sequence depth
updateMethod	smooth or noupdate (default 'smooth')

wbaopaul/limacc documentation built on Jan. 4, 2022, 2:31 a.m.