readBismark-method: readBismark method

In DMCHMM: Differentially Methylated CpG using Hidden Markov Model

Description

reads BS-Seq data

Usage

readBismark(files, colData, mc.cores)

## S4 method for signature 'character,DataFrame,numeric'
readBismark(files, colData, mc.cores)

## S4 method for signature 'character,data.frame,numeric'
readBismark(files, colData, mc.cores)

## S4 method for signature 'character,character,numeric'
readBismark(files, colData, mc.cores)

Arguments

files	A character list
colData	Object of class "DataFrame" containing information on variable values of the samples
mc.cores	An integer greater than 0

Value

A BSData-class object

Author(s)

Farhad Shokoohi <[e-mail]>

Examples

fn <- list.files(system.file('extdata',package = 'DMCHMM'))
fn.f <- list.files(system.file('extdata',package='DMCHMM'), full.names=TRUE)
OBJ <- readBismark(fn.f, fn, mc.cores=2)
cdOBJ <- DataFrame(Cell = factor(c('BC', 'TC','Mono'),
labels = c('BC', 'TC', 'Mono')), row.names = c('BCU1568','BCU173','BCU551'))
colData(OBJ) <- cdOBJ
OBJ

DMCHMM documentation built on Nov. 8, 2020, 8:20 p.m.