cool2matrix: converting cooler format to Hi-C matrices

In MonkeyLB/hicrep: Measuring the reproducibility of Hi-C data

Description

converting cooler format to Hi-C matrices

Usage

cool2matrix(file, chr = "chr1")

Arguments

file	the cooler file to be converted.
chr	specifiy which chr to be compared. Default is "chr1".

Value

a squared HiC matrix that can be recongnized by get.scc.

References

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient. Tao Yang, Feipeng Zhang, Galip Gurkan Yardimci, Fan Song, Ross C Hardison, William Stafford Noble, Feng Yue, Qunhua Li. Genome Research 2017. doi: 10.1101/gr.220640.117

Examples

## Not run: 
<<<<<<< HEAD
  # Read a .cool file, extract intrachromosomal interactions
=======
  # Read a .cool file, extract intrachromosomal interactions 
>>>>>>> 5fb05fb8f2e2c0a6bf86ed081614d280cfd0e0b6
  # on chr18 and convert it into a squared matrix
  mat <- cool2matrix(“hic.cool”, chr = ‘chr18’)

## End(Not run)

MonkeyLB/hicrep documentation built on Dec. 15, 2020, 12:47 a.m.