methylKit (version 0.99.2)

methylRawListDB-class: 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 read function.

Slots

treatment

numeric vector denoting control and test samples

.Data

a list of methylRawDB objects

Examples

# NOT RUN {
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)

# }