juicer2mat: calculate the reproducibility of HiChIP data in .hic format...

In TankKuma96/DisplayHiCRep:

Description

calculate the reproducibility of HiChIP data in .hic format and display all inter-chromosome and intra-chromosome in data frame and heat map

Usage

juicer2mat(dic, chromfile_path, pat1 = "_r1", pat2 = "_r2", len,
  maxrange = 5e+06, resolution = 5e+05, mapHeat = TRUE)

Arguments

dic	path of the contant maps exist
chromfile_path	a file that contain chromosome length information that is used for calculating bin size
pat1	pattern of files for chromosome 1. Default is "_r1".
pat2	pattern of files for chromosome 2. Default is "_r2".
len	amount of chromosome that will be compared about, which count from chr1
maxrange	An integer indicating the maximum distance of interaction that is considered. Default is 5000000.
resolution	An integer indicating the resolution level of the HiChIP matrix. Default is 500000.
mapHeat	If need to display in heat map or not. Default is TRUE

Value

matrix giving number of all inter-chromosome and intra-chromosome comparasion

TankKuma96/DisplayHiCRep documentation built on May 16, 2019, 3:06 p.m.