extractGC {DMRcaller} | R Documentation |
This function extracts GC sites in the genome
extractGC(methylationData, genome, contexts = c("ALL", "CG", "CHG", "CHH"))
methylationData |
the methylation data stored as a |
genome |
a BSgenome with the DNA sequence of the organism |
contexts |
the context in which the DMRs are computed ( |
the a subset of methylationData
consisting of all GC sites.
Ryan Merritt
## 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)