readENCODEdata: Reads in ENCODE RRBS data

In TomMayo/M3Ddevel: (development for M3D) Identifies differentially methylated regions across testing groups

Description

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

Usage

readENCODEdata(files, colData, 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.
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 [e-mail]

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 <- readENCODEdata(files,colData)

TomMayo/M3Ddevel documentation built on May 9, 2019, 4:53 p.m.