readBismark: Read Bismark

In DMRcaller: Differentially Methylated Regions caller

Description

This function takes as input a CX report file produced by Bismark and returns a GRanges object with four metadata columns The file represents the bisulfite sequencing methylation data.

Usage

readBismark(file)

Arguments

file	The filename (including path) of the methylation (CX report generated by Bismark) to be read.

Value

the methylation data stored as a GRanges object with four metadata columns (see methylationDataList).

Author(s)

Nicolae Radu Zabet and Jonathan Michael Foonlan Tsang

Examples

# load methylation data object
data(methylationDataList)

# save the one datasets into a file
saveBismark(methylationDataList[["WT"]], "chr3test_a_thaliana_wt.CX_report")

# load the data
methylationDataWT <- readBismark("chr3test_a_thaliana_wt.CX_report")

#check that the loading worked
all(methylationDataWT == methylationDataList[["WT"]])

Example output

Loading required package: GenomicRanges
Loading required package: stats4
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, sd, var, xtabs

The following objects are masked from ‘package:base’:

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

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Reading file: chr3test_a_thaliana_wt.CX_report
Read 374952 records
Finished reading file: chr3test_a_thaliana_wt.CX_report
[1] TRUE

DMRcaller documentation built on Nov. 8, 2020, 5:26 p.m.