HiCdata2matrix {coMET} | R Documentation

## Creates a HiC matrix from a file (Rao et al., 2014)

### Description

Creates a HiC matrix from Rao et al.,2014.

### Usage

    HiCdata2matrix( chr, start, end, bedFilePath)

### Arguments

`chr` | The chromosome of interest
`start` | The starting position in the region of interest (the smallest value)
`end` | The end position in the region of interest (the largest value)
`bedFilePath` | The path of the BED file from Kheradpour and Kellis, 2014.

### Value

An AnnotationTrack object of Gviz

### Author(s)

Tiphaine Martin

### References

http://bioconductor.org/packages/release/bioc/html/Gviz.html

Got to BindingMotifsBiomart binding motif biomart

### Examples

    library("corrplot")
    gen <- "hg19"
    chr<-"chr1"
    start <- 5000000
    end <- 9000000

    extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
    bedFilePath <- file.path(extdata, "HiC/chr1_1mb.RAWobserved")

    if(interactive()){
      matrix_HiC_Rao <- HiCdata2matrix(chr,start, end, bedFilePath)
    cor_matrix_HiC <- cor(matrix_HiC_Rao)
    diag(cor_matrix_HiC)<-1
    corrplot(cor_matrix_HiC, method = "circle")
    } else {
      data(matrix_HiC_Rao)
      cor_matrix_HiC <- cor(matrix_HiC_Rao)
    diag(cor_matrix_HiC)<-1
    corrplot(cor_matrix_HiC, method = "circle")
    }

[Package coMET version 1.12.0 Index]