addDiffMethTable-RnBDiffMeth-methods: addDiffMethTable-methods

In RnBeads: RnBeads

Description

Adds a differential methylation table

Usage

## S4 method for signature 'RnBDiffMeth'
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

Note

Caveat: if disk dumping is enabled the resulting object tables will be stored in the initial location of the object.

Author(s)

Fabian Mueller

Examples

library(RnBeads.hg19)
data(small.example.object)
logger.start(fname=NA)
dm <- rnb.execute.computeDiffMeth(rnb.set.example,"Sample_Group",c("genes","tiling"))
s.groups <- rnb.sample.groups(rnb.set.example,"Sample_Group")[[1]]
dmt.sites <- computeDiffTab.extended.site(meth(rnb.set.example),s.groups[[1]],s.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)

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