performLolaEnrichment.diffMeth {RnBeads} | R Documentation |
performs LOLA enrichment analysis for a given differential methylation table.
performLolaEnrichment.diffMeth( rnbSet, diffmeth, lolaDbPaths, rank.cuts.region = c(100, 500, 1000), add.auto.rank.cut = TRUE, rerank = TRUE, verbose = TRUE )
rnbSet |
RnBSet object for which dirrential methylation was computed |
diffmeth |
RnBDiffMeth object. See |
lolaDbPaths |
LOLA database paths |
rank.cuts.region |
Cutoffs for combined ranking that are used to determine differentially methylated regions |
add.auto.rank.cut |
flag indicating whether an automatically computed cut-off should also be considered. |
rerank |
For deterimining differential methylation: should the ranks be ranked again or should the absolute ranks be used. |
verbose |
Enable for detailed status report |
a DiffMeth.lola.enrich object (S3) containing the following attributes
region |
Enrichment information for differential methylation on the region level. A |
lolaDb |
The loaded |
Fabian Mueller
library(RnBeads.hg19) data(small.example.object) logger.start(fname=NA) # compute differential methylation dm <- rnb.execute.computeDiffMeth(rnb.set.example,pheno.cols=c("Sample_Group","Treatment")) # download LOLA DB lolaDest <- tempfile() dir.create(lolaDest) lolaDirs <- downloadLolaDbs(lolaDest, dbs="LOLACore") # perform enrichment analysis res <- performLolaEnrichment.diffMeth(rnb.set.example,dm,lolaDirs[["hg19"]])