get.table,RnBDiffMeth-method {RnBeads} | R Documentation |
Gets a differential methylation table
## S4 method for signature 'RnBDiffMeth' get.table( object, comparison, region.type, undump = TRUE, return.data.frame = FALSE )
object |
|
comparison |
character or index of the comparison of the table to retrieve |
region.type |
character or index of the region type of the table to retrieve |
undump |
Flag indicating whether to convert the table into a matrix instead of using the file descriptor.
Only meaningful if the if the objects's |
return.data.frame |
should a data.frame be returned instead of a matrix? |
differential methylation table. See computeDiffMeth.bin.site
and computeDiffMeth.bin.region
for details.
Fabian Mueller
library(RnBeads.hg19) data(small.example.object) logger.start(fname=NA) dm <- rnb.execute.computeDiffMeth(rnb.set.example,pheno.cols=c("Sample_Group","Treatment")) dm.promoters <- get.table(dm,get.comparisons(dm)[1],"promoters",return.data.frame=TRUE) summary(dm.promoters)