This function is a wrapper function to identify partially methylated domains (PMDs) in Bis-seq data.
Usage
## S4 method for signature 'methylPipe,BSdata'
findPMDs(Object, Nproc=1, Chrs=NULL)
Arguments
Object
An object of class BSdataSet
Nproc
numeric; the number of processors to use, one chromosome
is ran for each processor
Chrs
character; Chromosome on which PMDs are identified
Details
This functions is a wrapper function of segmentPMDs method of package MethylSeekR.
This function trains a Hidden Markov Model (HMM) to detect partially methylated domains (PMDs) in Bis-seq data.
Value
A GRangesList object containing segments that partition the genome
into PMDs and regions outside of PMDs. The object contains two
metadata columns indicating the type of region (PMD/notPMD) and
the number of covered (by at least 5 reads) CpGs (nCG) in the
region.
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)
R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(methylPipe)
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: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/methylPipe/findPMDs.Rd_%03d_medium.png", width=480, height=480)
> ### Name: findPMDs
> ### Title: Identifying Partially Methylated Domains (PMDs)
> ### Aliases: findPMDs findPMDs,methylPipe,BSdata
> ### findPMDs,methylPipe,BSdata-method findPMDs-methods
> ### findPMDs,BSdata-method
>
> ### ** Examples
>
> require(BSgenome.Hsapiens.UCSC.hg18)
Loading required package: BSgenome.Hsapiens.UCSC.hg18
Loading required package: BSgenome
Loading required package: rtracklayer
> uncov_GR <- GRanges(Rle('chr20'), IRanges(c(14350,69251,84185), c(18349,73250,88184)))
> H1data <- system.file('extdata', 'H1_chr20_CG_10k_tabix_out.txt.gz', package='methylPipe')
> H1.db <- BSdata(file=H1data, uncov=uncov_GR, org=Hsapiens)
> PMDs <- findPMDs(H1.db, Nproc=1, Chrs="chr20")
>
>
>
>
>
> dev.off()
null device
1
>