getGM12878 {REMP} | R Documentation |
getGM12878
is used to obtain public available methylation profiling
data of HapMap LCL sample GM12878.
getGM12878(arrayType = c("450k", "EPIC"), mapGenome = FALSE)
arrayType |
Illumina methylation array type. Currently |
mapGenome |
Logical parameter. If |
Illumina 450k data were sourced and curated from ENCODE
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450Gm12878SitesRep1.bed.gz.
Illumina EPIC data were obtained from data package minfiDataEPIC
.
A RatioSet
or GenomicRatioSet
containing
beta value and M value of the methylation data.
# Get GM12878 methylation data (EPIC array) GM12878_EPIC <- getGM12878('EPIC') GM12878_EPIC