readBedFiles {M3D}R Documentation

Reads in bed file to make RRBS data

Description

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

Usage

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

Arguments

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.

Value

Returns a BSraw object storing methylation and coverage data - the underlying structure for this package.

Author(s)

Tom Mayo t.mayo@ed.ac.uk

Examples


# 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)

[Package M3D version 1.14.0 Index]