RnBeads (version 1.4.0)

addDiffMethTable,RnBDiffMeth-method: addDiffMethTable-methods

Description

Adds a differential methylation table

Usage

"addDiffMethTable"(object, dmt, comparison, region.type, grp.labs = c("group1", "group2"))

Arguments

object

RnBDiffMeth object

dmt

Differential methylation table to add

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

grp.labs

character vector of length 2 specifying the names of the groups being compared

Value

the updated RnBDiffMeth object

Examples

library(RnBeads.hg19)
data(small.example.object)
logger.start(fname=NA)
dm <- rnb.execute.computeDiffMeth(rnb.set.example,pheno.cols="Sample_Group",region.types=c("genes","tiling"))
sample.groups <- rnb.sample.groups(rnb.set.example,"Sample_Group")[[1]]
dmt.sites <- computeDiffTab.extended.site(meth(rnb.set.example),sample.groups[[1]],sample.groups[[2]])
map.regions.to.sites <- regionMapping(rnb.set.example,"promoters")
dmt.promoters <- computeDiffTab.default.region(dmt.sites,map.regions.to.sites)
cmp.name <- get.comparisons(dm)[1]
grp.labs <- get.comparison.grouplabels(dm)[1,]
#add the promoter level differential methylation table
dm.add <- addDiffMethTable(dm,dmt.promoters,cmp.name,"promoters",grp.labs)
get.region.types(dm.add)