inflateMethylome: Inflate an imported methylation extractor file

In methimpute: Imputation-guided re-construction of complete methylomes from WGBS data

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

methimpute documentation built on Nov. 8, 2020, 5:47 p.m.