visHiCDB: Visualization of CDBs or differential CDBs on Hi-C maps

In ChenFengling/RHiCDB: RHiCDB detects contact domain boundaries(CDB) on Hi-C matrix

Description

visHiCDB uses Hi-C raw contact matrix and CDBs as input and outputs figures of CDBs or differential CDBs on Hi-C maps

Usage

visHiCDB(hicfile, CDBfile, resolution, chr, startloc, endloc, outdir)

Arguments

hicfile	hicfile is the file names of the intra-chromosome matrixes. The intra-chromosome matrix could be in a dense (a NxN matrix) or sparse (a Kx3 table,Rao et al.) format. Show CDBs on one sample,set hicfile as 'SAMPLE_File'. Show differebtial CDBs in two samples, set hicfile as list('SAMPLE1_FILE','SAMPLE2_FILE').
CDBfile	CDBfile should be is file name of the CDB files. Show CDBs on one sample,set CDBfile as 'SAMPLE_CDB'. Show differebtial CDBs in two samples, set CDBfile as list('SAMPLE1_CDB','SAMPLE2_CDB'). The CDB file should be formated as the output file of HiCDB.
resolution	resolution of Hi-C matrix. This is required.
chr, startloc, endloc	numeric observation locus on Hi-C map.This is required.
outdir	The output direction. Default will be the directory of the first sample.

Details

This function outputs a pdf figure showing CDBs on a Hi-C map on desired locus. Conserved CDBs are marked as dark blue.

Author(s)

Implemented by Fengling Chen

Any suggestions and remarks might be addressed to Fengling Chen:[e-mail]

Examples

     ## Show CDB on single Hi-C map
     visHiCDB('sample1/chr18.matrix','CDB1.txt',40000,18,25000000,31150000)
     ## Show differential CDBs
     visHiCDB(list('sample1/chr18.matrix','sample2/chr18.matrix'),
        +list('CDB1.txt','CDB2.txt'),40000,18,25000000,31150000)

ChenFengling/RHiCDB documentation built on June 7, 2020, 12:42 a.m.