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Last data update: 2014.03.03

R: Exploratory statistics of samples in BSdataSet object

methstats

R Documentation

Exploratory statistics of samples in BSdataSet object

Description

Exploratory methylation statistics of samples in BSdataSet object.

Usage

## S4 method for signature 'methylPipe,BSdataSet'
methstats(object, chrom, mcClass='mCG', minC=1, coverage=1, pval=1, Nproc=1)

Arguments

`object`	An object of class BSdataSet
`chrom`	character; either NULL or an object of class character
`mcClass`	character; the mC sequence context to be considered, one of all, mCG, mCHG or mCHH
`minC`	numeric; the minumum number of reads with C (DNA-methylation events) at a given cytosine genomic position
`coverage`	numeric; the minimum number of total reads at a given cytosine genomic position
`pval`	numeric; the minimum binomial pValue for an mC call at a given cytosine genomic position
`Nproc`	numeric; the number of processors to use, one chromosome is ran for each processor

Details

The function provides basic statistical methods which computes descriptive statistics, correlation matrix and clustering of samples within the BSdataSet.

Value

A list with slots named descriptive_stats and correlation_mat.

Author(s)

Kamal Kishore

Examples

require(BSgenome.Hsapiens.UCSC.hg18)
uncov_GR <- GRanges('chr20', IRanges(14350, 18349))
H1data <- system.file('extdata', 'H1_chr20_CG_10k_tabix_out.txt.gz', package='methylPipe')
H1.db <- BSdata(file=H1data, uncov=uncov_GR, org=Hsapiens)
IMR90data <- system.file('extdata', 'IMR90_chr20_CG_10k_tabix_out.txt.gz', package='methylPipe')
IMR90.db <- BSdata(file=IMR90data, uncov=uncov_GR, org=Hsapiens)
H1.IMR90.set <- BSdataSet(org=Hsapiens, group=c("C","C","E","E"), IMR_1=IMR90.db, 
IMR_2=IMR90.db, H1_1=H1.db,H1_2=H1.db)
stats_res <- methstats(H1.IMR90.set,chrom="chr20",mcClass='mCG', Nproc=1)
stats_res

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> 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/methstats.Rd_%03d_medium.png", width=480, height=480)
> ### Name: methstats
> ### Title: Exploratory statistics of samples in BSdataSet object
> ### Aliases: methstats methstats,methylPipe,BSdataSet
> ###   methstats,methylPipe,BSdataSet-method methstats-methods
> ###   methstats,BSdataSet-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('chr20', IRanges(14350, 18349))
> H1data <- system.file('extdata', 'H1_chr20_CG_10k_tabix_out.txt.gz', package='methylPipe')
> H1.db <- BSdata(file=H1data, uncov=uncov_GR, org=Hsapiens)
> IMR90data <- system.file('extdata', 'IMR90_chr20_CG_10k_tabix_out.txt.gz', package='methylPipe')
> IMR90.db <- BSdata(file=IMR90data, uncov=uncov_GR, org=Hsapiens)
> H1.IMR90.set <- BSdataSet(org=Hsapiens, group=c("C","C","E","E"), IMR_1=IMR90.db, 
+ IMR_2=IMR90.db, H1_1=H1.db,H1_2=H1.db)
> stats_res <- methstats(H1.IMR90.set,chrom="chr20",mcClass='mCG', Nproc=1)
Error in dev.new() : no suitable unused file name for pdf()
Calls: methstats -> methstats -> dev.new
Execution halted