RnBeads (version 1.4.0)

get.table,RnBDiffMeth-method: get.table-methods

Description

Gets a differential methylation table

Usage

"get.table"(object, comparison, region.type, undump = TRUE, return.data.frame = FALSE)

Arguments

object

RnBDiffMeth 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 disk.dump slot is true.

return.data.frame

should a data.frame be returned instead of a matrix?

Value

differential methylation table. See computeDiffMeth.bin.site and computeDiffMeth.bin.region for details.

Examples

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)