get.table-RnBDiffMeth-methods: get.table-methods

In RnBeads: RnBeads

Description

Gets a differential methylation table

Usage

## S4 method for signature 'RnBDiffMeth'
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.

Author(s)

Fabian Mueller

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)

RnBeads documentation built on March 3, 2021, 2 a.m.