Class "BSdata"

Description

This class is used in the methylPipe library to point to a TABIX compressed file containing base-resolution DNA-methylation data and reference genome sequence

Objects from the Class

Objects can be created by calls of the form new("BSdata", ...) or using the function BSdata(file, uncov, org) whose arguments are described in the next section Slots.

Slots

file:

Object of class "character" : the TABIX compressed file containing base-resolution DNA-methylation data. This file can be generated through the BSprepare function, and it must contain the following columns: chromosome assignment (in the form chr1, chr2...), genomic position (positive integer), strand (either - or +), methylation sequence context (either CG, CHG or CHH), number (>0) of sequencing reads with C calls at that genomic position, number of sequencing reads with T calls at that genomic position, binomial pvalue (-10*log10(pvalue)) for calling a mC at that position.

uncov:

Object of class GRanges : this GRanges object consists of the list of genomic regions with sequencing coverage information; this information is used to distinguish which methylation sites are unmethylated, but covered, from those that are missing data since they have no sequencing coverage. This object is automatically generated by the meth.call function while processing aligned files generated from the aligner.

org:

refrence genome of class BSgenome

Author(s)

Mattia Pelizzola

See Also

BSprepare,mCsmoothing

Examples

require(BSgenome.Hsapiens.UCSC.hg18)
H1data <- system.file('extdata', 'H1_chr20_CG_10k_tabix_out.txt.gz', package='methylPipe')
uncov_GR <- GRanges(Rle('chr20'), IRanges(c(14350,69251,84185), c(18349,73250,88184)))
H1.db <- BSdata(file=H1data, uncov=uncov_GR, org=Hsapiens)

Results

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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/BSdata-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: BSdata-class
> ### Title: Class "BSdata"
> ### Aliases: BSdata-class BSdata show,BSdata-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> require(BSgenome.Hsapiens.UCSC.hg18)
Loading required package: BSgenome.Hsapiens.UCSC.hg18
Loading required package: BSgenome
Loading required package: rtracklayer
> H1data <- system.file('extdata', 'H1_chr20_CG_10k_tabix_out.txt.gz', package='methylPipe')
> uncov_GR <- GRanges(Rle('chr20'), IRanges(c(14350,69251,84185), c(18349,73250,88184)))
> H1.db <- BSdata(file=H1data, uncov=uncov_GR, org=Hsapiens)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>