HiCdata2matrix: Creates a HiC matrix from a file (Rao et al., 2014)

In TiphaineCMartin/coMET_original: coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns.

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")
}

TiphaineCMartin/coMET_original documentation built on May 9, 2019, 4:49 p.m.