extractGC: Extract GC

In nrzabet/DMRcaller: Differentially Methylated Regions caller

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)){
  if (!requireNamespace("BiocManager", quietly=TRUE))
      install.packages("BiocManager")
  BiocManager::install("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)

nrzabet/DMRcaller documentation built on May 23, 2019, 2:50 p.m.