exportDMRs2regionFile {RnBeads} | R Documentation |
export differentially methylated regions to region file (standard bed). The output is in BED6 format where the score corresponds to to the combined rank (rank==1 would receive a score of 1000 and a combined rank equal to the number of regions a score of 0)
exportDMRs2regionFile( rnbSet, diffmeth, dest, comp.name, region.type, rank.cut = NULL, rerank = FALSE )
rnbSet |
the RnBSet object for which the DMRs were computed. |
diffmeth |
DiffMeth object. See |
dest |
destination file name |
comp.name |
name of the comparison |
region.type |
region type. |
rank.cut |
rank cutoff. If |
rerank |
flag indicating whether the ranks should be reranked or whether |
NULL
Fabian Mueller
library(RnBeads.hg19) data(small.example.object) logger.start(fname=NA) dm <- rnb.execute.computeDiffMeth(rnb.set.example,pheno.cols=c("Sample_Group","Treatment")) exportDMRs2regionFile(rnb.set.example,dm,tempfile(),get.comparisons(dm)[1],"promoters")