extract-methods: extract parts of...

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

extract parts of methylRaw,methylRawDB,methylBase,methylBaseDB and methylDiff data

Description

The function extracts part of the data and returns a new object.

Usage

## S4 method for signature 'methylRaw,ANY,ANY,ANY'
x[i, j]

## S4 method for signature 'methylBase,ANY,ANY,ANY'
x[i, j]

## S4 method for signature 'methylDiff,ANY,ANY,ANY'
x[i, j]

## S4 method for signature 'methylRawDB,ANY,ANY,ANY'
x[i, j]

## S4 method for signature 'methylBaseDB,ANY,ANY,ANY'
x[i, j]

## S4 method for signature 'methylDiffDB,ANY,ANY,ANY'
x[i, j]

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.
j	This argument can not be used for the extraction of columns. As unintentional extraction of the columns will cause an error in the downstream analysis. Using this argument will cause an error. Use getData to access the data part of the objects.

Examples

data(methylKit)

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

# selects first hundred rows, returns a methylBase object
subset2=methylBase.obj[1:100,] 

# selects first hundred rows, returns a methylDiff object
subset3=methylDiff.obj[1:100,] 

# This will get chromomsomes, will return a factor
# That means the resulting object will ceases to be a methylKit object
chrs=methylDiff.obj[[2]]

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