importRene: Import a Rene methylation extractor file

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

Description

Import a Rene methylation extractor file into a GRanges-class object.

Usage

importRene(file, chrom.lengths = NULL, skip = 1)

Arguments

file	The file to import.
chrom.lengths	A data.frame with chromosome names in the first, and chromosome lengths in the second column. Only chromosomes named in here will be returned. Alternatively a tab-separated file with such a data.frame (with headers).
skip	The number of lines to skip. Usually 1 if the file contains a header and 0 otherwise.

Value

A methimputeData object.

Examples

## Get an example file in Rene format
file <- system.file("extdata","arabidopsis_rene.txt", package="methimpute")
data(arabidopsis_chromosomes)
rene.data <- methimpute:::importRene(file, chrom.lengths=arabidopsis_chromosomes)

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