getHiCMatrix: Grab a specific sparse Hi-C matrix

In aryeelab/sparseHiC: Efficient compression and analysis of Hi-C Data

Description

getHiCMatrix takes a sparseHiCdatum object and returns a single matrix. Thus, the length of chr and res must be 1

Usage

getHiCMatrix(obj, chr, res, sampleName)

## S4 method for signature 'sparseHiCdatum'
getHiCMatrix(obj, chr, res, sampleName)

## S4 method for signature 'sparseHiCdata'
getHiCMatrix(obj, chr, res, sampleName)

Arguments

obj	A sparseHiCdatum object
chr	Chromosome desired
res	Resolution desired
sampleName	When accessing a matrix with multiple samples in the object

Value

Returns a Hi-C Matrix

Examples

chr <- "chr21"
res <- "1000000"

#Single sample
rds<-paste(system.file('rds',package='sparseHiC'),'hESCdatum1.rds',sep='/')
hESCdatum1 <- readRDS(rds)
r <- getHiCMatrix(hESCdatum1,chr = chr, res = res) 

rdsA<-paste(system.file('rds',package='sparseHiC'),'hESCdata.rds',sep='/')
hESCdata <- readRDS(rdsA)
getHiCMatrix(hESCdata, chr = chr, res = res, sampleName = "hESC2") 

aryeelab/sparseHiC documentation built on May 12, 2019, 3:43 a.m.