methylRawListDB-class: An S4 class for holding a list of methylRawDB objects.

In al2na/methylKit: DNA methylation analysis from high-throughput bisulfite sequencing results

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)

Arguments

...	vector of methylRawDB files
treatment	vector of treatment values

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)

al2na/methylKit documentation built on Feb. 1, 2024, 4:42 p.m.