BSdataSet-class {methylPipe} | R Documentation

## 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)

[Package methylPipe version 1.20.0 Index]