select-methods: selects rows from of methylKit objects

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

selects rows from of methylKit objects

Description

The function returns a subset of data contained in the methylKit objects.

Usage

select(x,i)

## S4 method for signature 'methylBase'
select(x, i)

## S4 method for signature 'methylRaw'
select(x, i)

## S4 method for signature 'methylDiff'
select(x, i)

## S4 method for signature 'methylRawDB'
select(x, i)

## S4 method for signature 'methylBaseDB'
select(x, i)

## S4 method for signature 'methylDiffDB'
select(x, i)

Arguments

x	an methylBase,methylBaseDB, methylRaw,methylRawDB or methylDiff object
i	a numeric or logical vector. This vector corresponds to bases or regions contained in methylKit objects.The vector is used to subset the data.

Value

a methylBase,methylRaw or methylDiff object depending on the input object.

Examples

data(methylKit)


methylRawDB.obj=methRead( system.file("extdata","test1.txt.bgz",package="methylKit"),
                          sample.id="test1", assembly="hg18",
                          dbtype = "tabix",dbdir = "methylDB")

methylBaseDB.obj=unite(methylRawList.obj,save.db=TRUE,dbdir="methylDB")


 # selects first hundred rows, returns a methylRaw object
subset1=select(methylRawList.obj[[1]],1:100)
subset1=select(methylRawDB.obj,1:100)

# selects first hundred rows, returns a methylBase object
subset2=select(methylBase.obj,1:100) 
subset2=select(methylBaseDB.obj,1:100)

# selects first hundred rows, returns a methylDiff object
subset3=select(methylDiff.obj,1:100)




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

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