inflateMethylome: Inflate an imported methylation extractor file

Description Usage Arguments Value Examples

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

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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

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## 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

ataudt/popmeth documentation built on May 10, 2019, 2:07 p.m.