countGC {charm} | R Documentation |
Return the GC content for each probe
countGC(dat, type = "pm", idx)
dat |
a TilingFeatureSet object |
type |
pm or bg probes |
idx |
An optional vector of probe indices for which to return GC content. If not specified, values for all pm (or bg) probes will be returned. |
This function returns the sum of #G + #C in the pm or bg probes.
a numeric vector
Martin Aryee <aryee@jhu.edu>
if (require(charmData)) { phenodataDir <- system.file("extdata", package="charmData") pd <- read.delim(file.path(phenodataDir, "phenodata.txt")) pd <- subset(pd, sampleID=="441_liver") dataDir <- system.file("data", package="charmData") setwd(dataDir) rawData <- readCharm(files=pd$filename, sampleKey=pd) ngc <- countGC(rawData) head(ngc) }