readBedFiles: Reads in bed file to make RRBS data
In M3D: Identifies differentially methylated regions across testing groups

Description Usage Arguments Value Author(s) Examples

Reads in RRBS data in bed file format from various styles and outputs an rrbs data structure. Adapted from readBismark in the BiSeq package.

1	readBedFiles(files, colData, bed_type = "Encode", eData = NaN)

`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
`eData`	Experiment data to describe the work. This is used to create the BSraw object as in the BiSeq package.

Returns a BSraw object storing methylation and coverage data - 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 <- readBedFiles(files,colData)