methylRawListDB-class {methylKit} | R Documentation

## An S4 class for holding a list of methylRawDB objects.

### Description

This class stores the list of `methylRawDB` objects. Functions such as `lapply` can be used on this list. It extends `list` class. This object is primarily produced by `methRead` function.

### Usage

    methylRawListDB(..., treatment)

### Slots

`treatment`

  numeric vector denoting control and test samples

`.Data`

  a list of `methylRawDB` objects

### Constructor

`methylRawListDB(...)`

  combine multiple methylRawDB objects supplied in ... into a methylRawListDB object.

### Examples

    file.list=list( system.file("extdata", "test1.myCpG.txt",
    package = "methylKit"),
                    system.file("extdata", "test2.myCpG.txt",
                    package = "methylKit"),
                    system.file("extdata", "control1.myCpG.txt",
                    package = "methylKit"),
                    system.file("extdata", "control2.myCpG.txt",
                    package = "methylKit") )

    methylRawListDB.obj <- methRead(file.list,
    sample.id = list("test1","test2","ctrl1","ctrl2"),
                                assembly = "hg18",treatment = c(1,1,0,0),
                                dbtype = "tabix",dbdir = "methylDB")

    #applying functions designed for methylRawDB on methylRawListDB object
    lapply(methylRawListDB.obj,"getAssembly")

    # remove Database again
    rm(methylRawListDB.obj)
    unlink("methylDB",recursive=TRUE)

[Package methylKit version 1.18.0 Index]