readBedRaw {M3D} | R Documentation |
Reads in RRBS data in bed file format from a variety of formats and outputs a list that is turned into an rrbs data structure in the wrapper function. Adapted from readBismark in the BiSeq package.
readBedRaw(files, colData, bed_type = "Encode")
files |
A character pointing the the rrbs files downloads from the ENCODE database. |
colData |
Samples' names plus additional sample information as character, data.frame or DataFrame. |
bed_type |
Character string representing the style of the bed file. Options are |
Returns a list with all the data that will be turned into a BSraw object - the underlying structure for this package.
Tom Mayo t.mayo@ed.ac.uk
# download the files and change the working directory # to that location files <- c('wgEncodeHaibMethylRrbsH1hescHaibSitesRep1.bed.gz', 'wgEncodeHaibMethylRrbsH1hescHaibSitesRep2.bed.gz', 'wgEncodeHaibMethylRrbsK562HaibSitesRep1.bed.gz', 'wgEncodeHaibMethylRrbsK562HaibSitesRep2.bed.gz') group <- factor(c('H1-hESC','H1-hESC','K562','K562')) samples <- c('H1-hESC1','H1-hESC2','K562-1','K562-2') colData <- DataFrame(group,row.names= samples) rrbs <- readBedRaw(files,colData)