readMethylome: Load Bis-seq data

In MethylSeekR: Segmentation of Bis-seq data

Description

Loading Bis-seq data from tab-delimited file or saved GRanges object

Usage

readMethylome(FileName, seqLengths, format = "text")

Arguments

FileName	File name.
seqLengths	A named vector indicating the chromosome lengths of the genome used.
format	File format. If format is set to "text" (default), the argument FileName should refer to a tab-delimited text file in the format: chromosome position T M, where each line stands for a CpG, the position refers to the C of the CpG (on the plus strand), T is the total number of reads (total counts) covering the CpG and M the total number of reads without C to T conversion at the C of the CpG (methylation counts). If format="GRanges", the file is assumed to be a GRanges object, containing T and M as first and second data-value entries, saved in rds format.

Value

A GRanges object containing the coordinates, total (T) and methylated counts (M)

Author(s)

Lukas Burger [e-mail]

Examples

library(MethylSeekR)

# get chromosome lengths
library("BSgenome.Hsapiens.UCSC.hg18")
sLengths=seqlengths(Hsapiens)

# read methylation data
methFname <- system.file("extdata", "Lister2009_imr90_hg18_chr22.tab",
package="MethylSeekR")
meth.gr <- readMethylome(FileName=methFname, seqLengths=sLengths)

MethylSeekR documentation built on Nov. 8, 2020, 6:57 p.m.