LiMACC: call LiMACC algorithm
In wbaopaul/limacc: LiMACC

Description Usage Arguments

call LiMACC algorithm

LiMACC(index_file, count_file, out_filename, comb_rep = "merge",
  dtype = "CHiC", peakFile4HiChIP = NULL, numG = 100,
  hcrc_pr = 0.9, fdr = 0.1, nIter = 20, maxN = 10000,
  minLen = NULL, maxLen = NULL, minDist = NULL, maxDist = 2 * 10^6,
  adj.method = "IHW", adjSeqDepth = NULL, updateMethod = "smooth")

`index_file`	the name of restriction enzyme file for CHiC or index_file for HiChIP
`count_file`	contact map file(s)
`out_filename`	output file name
`comb_rep`	if length(count_file)>1, merge or pool replicates (default merge for CHiC; pool for HiChIP)
`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
`numG`	number of groups for limacc (default 100)
`hcrc_pr`	initial guess of backgound (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 100)
`minLen`	filter otherEnd fragments with length smaller than minLen
`maxLen`	filter otherEnd fragments with length greater than maxLen
`adj.method`	method for adjusting p-value (default 'IHW')
`updateMethod`	smooth or noupdate (default 'smooth')
`sdepth`	the number (in million) to which the sequence depth should be normalized, default NULL means do not adjust the total sequence depth