readMethylome {MethylSeekR} | R Documentation

## Load 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 lukas.burger@fmi.ch

### 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)

[Package MethylSeekR version 1.20.0 Index]