R: Inflate an imported methylation extractor file

inflateMethylome {methimpute}

R Documentation

Inflate an imported methylation extractor file

Description

Inflate an imported methylation extractor file to contain all cytosine positions. This is useful to obtain a full methylome, including non-covered cytosines, because most methylation extractor programs only report covered cytosines.

Usage

inflateMethylome(methylome, methylome.full)

Arguments

`methylome`	A `GRanges-class` with methylation counts.
`methylome.full`	A `GRanges-class` with positions for all cytosines or a file with such an object.

Value

The methylome.full object with added metadata column 'counts'.

Examples

## Get an example file in BSSeeker format
file <- system.file("extdata","arabidopsis_bsseeker.txt.gz", package="methimpute")
bsseeker.data <- importBSSeeker(file)
bsseeker.data

## Inflate to full methylome (including non-covered sites)
data(arabidopsis_toydata)
full.methylome <- inflateMethylome(bsseeker.data, arabidopsis_toydata)
full.methylome

[Package methimpute version 1.4.1 Index]