reorganize-methods: Reorganize methylKit objects by creating new objects from...

In fortunatobianconi/methylkit: DNA methylation analysis from high-throughput bisulfite sequencing results

Description

The function creates a new methylRawList or methylBase object by selecting a subset of samples from the input object, which is a methylRawList or methylBase object. You can use the function to partition a large methylRawList or methylBase object to smaller object based on sample ids or when you want to reorder samples and/or give a new treatmet vector.

Usage

  reorganize(methylObj,sample.ids,treatment)

Arguments

methylObj	a methylRawList or methylBase object
sample.ids	a vector for sample.ids to be subset. Order is important and the order should be similar to treatment. sample.ids should be a subset or reordered version of sample ids in the input object.
treatment	treatment vector, should be same length as sample.ids vector

Value

returns a methylRawList or methylBase object depending on the input object

Examples

# this is a list of example files, ships with the package
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") )


# read the files to a methylRawList object: myobj
myobj=read( file.list,
          sample.id=list("test1","test2","ctrl1","ctrl2"),assembly="hg18",pipeline="amp",treatment=c(1,1,0,0))
meth=unite(myobj,destrand=TRUE)

# get samples named "test1" and "ctrl2" from myobj and create a new methylRawList object
myobj2=reorganize(myobj,sample.ids=c("test1","ctrl2"),treatment=c(1,0) )

# # get samples named "test1" and "ctrl2" from meth and create a new methylBase object
meth2 =reorganize(meth,sample.ids=c("test1","ctrl2"),treatment=c(1,0) )

fortunatobianconi/methylkit documentation built on May 16, 2019, 1:51 p.m.