Class "BSdataSet"

Description

This class is used in the methylPipe library to store a set of BSdata objects

Objects from the Class

Objects can be created by calls of the form new("BSdataSet", ...) or using the function BSdataSet(org,Objlist,names), see below.

Slots

Objlist:

Object of class "list" : a list with more than one item, where each item is a BSdata object

names:

Object of class "character" : vector of the names of the objects, i.e. the sample names

group:

Object of class "character" : indicating conditions and replicates; replicated samples within the same condition have to be assigned the same group name; if object has only two groups, "C"(control) and "E" (Experiment) should be specified as groups name

org:

refrence genome of class BSgenome

Methods

"[["

signature(x = "BSdataSet"): subsets the BSdataSet returning a specific BSdata object

"[[<-"

signature(x = "BSdataSet"): replaces the specific BSdata object in the BSdataSet

"["

signature(x = "BSdataSet"): subsets the BSdataSet returning another BSdataSet

Author(s)

Mattia Pelizzola, Kamal Kishore

See Also

BSdata-class,findDMR

Examples

require(BSgenome.Hsapiens.UCSC.hg18)
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)
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","E"), IMR90=IMR90.db, H1=H1.db)

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/BSdataSet-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: BSdataSet-class
> ### Title: Class "BSdataSet"
> ### Aliases: BSdataSet-class BSdataSet length,BSdataSet-method
> ###   show,BSdataSet-method [[<-,BSdataSet,ANY,ANY-method
> ###   [[,BSdataSet,ANY,ANY-method [,BSdataSet,ANY,ANY-method
> ###   $,BSdataSet-method $,BSdataSet
> ### Keywords: classes
> 
> ### ** 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)
> 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","E"), IMR90=IMR90.db, H1=H1.db)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>