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Last data update: 2014.03.03

R: Load Bis-seq data

readMethylome

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)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> library(MethylSeekR)
Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: mhsmm
Loading required package: mvtnorm
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MethylSeekR/readMethylome.Rd_%03d_medium.png", width=480, height=480)
> ### Name: readMethylome
> ### Title: Load Bis-seq data
> ### Aliases: readMethylome
> 
> ### ** Examples
> 
> 
> library(MethylSeekR)
> 
> # get chromosome lengths
> library("BSgenome.Hsapiens.UCSC.hg18")
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
> sLengths=seqlengths(Hsapiens)
> 
> # read methylation data
> methFname <- system.file("extdata", "Lister2009_imr90_hg18_chr22.tab",
+ package="MethylSeekR")
> meth.gr <- readMethylome(FileName=methFname, seqLengths=sLengths)
reading methylome data
Read 200000 records
> 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>