importRene: Import a Rene methylation extractor file

Description Usage Arguments Value Examples

Description

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

Usage

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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

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## 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)

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