addDiffMethTable,RnBDiffMeth-method {RnBeads} | R Documentation |
Adds a differential methylation table
## S4 method for signature 'RnBDiffMeth' addDiffMethTable( object, dmt, comparison, region.type, grp.labs = c("group1", "group2") )
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 |
the updated RnBDiffMeth object
Caveat: if disk dumping is enabled the resulting object tables will be stored in the initial location of the object.
Fabian Mueller
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)