limacc: LiMACC algorithm

Description Usage Arguments

Description

Identify significant chromatin interations for multiple chromosome conformation capture assays

Usage

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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.