R: Extract GC

extractGC {DMRcaller}

R Documentation

Extract GC

Description

This function extracts GC sites in the genome

Usage

extractGC(methylationData, genome, contexts = c("ALL", "CG", "CHG", "CHH"))

Arguments

`methylationData`	the methylation data stored as a `GRanges` object with four metadata columns (see `methylationDataList`).
`genome`	a BSgenome with the DNA sequence of the organism
`contexts`	the context in which the DMRs are computed (`"ALL"`, `"CG"`, `"CHG"` or `"CHH"`).

Value

the a subset of methylationData consisting of all GC sites.

Author(s)

Ryan Merritt

Examples


## Not run: 
# load the genome sequence
if(!require("BSgenome.Athaliana.TAIR.TAIR9", character.only = TRUE)){
  source("https://bioconductor.org/biocLite.R")
  biocLite("BSgenome.Athaliana.TAIR.TAIR9")
}
library(BSgenome.Athaliana.TAIR.TAIR9)

# load the methylation data
data(methylationDataList)

methylationDataWTGpCpG <- extractGC(methylationDataList[["WT"]], 
                                    BSgenome.Athaliana.TAIR.TAIR9,
                                    "CG")


## End(Not run)

[Package DMRcaller version 1.12.7 Index]