import: Methimpute data import

In ataudt/popmeth: Imputation-guided re-construction of complete methylomes from WGBS data

Description

This page provides an overview of all methimpute data import functions.

Usage

importBSMAP(file, chrom.lengths = NULL, skip = 1, contexts = c(CG =
  "NNCGN", CHG = "NNCHG", CHH = "NNCHH"))

importMethylpy(file, chrom.lengths = NULL, skip = 1, contexts = c(CG
  = "CGN", CHG = "CHG", CHH = "CHH"))

importBSSeeker(file, chrom.lengths = NULL, skip = 0)

importBismark(file, chrom.lengths = NULL, skip = 0)

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.
contexts	A character vector of the contexts that are to be assigned. Since some programs report 5-letter contexts, this parameter can be used to obtain a reduced number of contexts. Will yield contexts CG, CHG, CHH by default. Set contexts=NULL to obtain all available contexts.

Value

A methimputeData object.

Functions

• importBSMAP: Import a BSMAP methylation extractor file.

• importMethylpy: Import a Methylpy methylation extractor file.

• importBSSeeker: Import a BSSeeker methylation extractor file.

• importBismark: Import a Bismark methylation extractor file.

Examples

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

## Get an example file in Bismark format
file <- system.file("extdata","arabidopsis_bismark.txt", package="methimpute")
data(arabidopsis_chromosomes)
arabidopsis_chromosomes$chromosome <- sub('chr', '', arabidopsis_chromosomes$chromosome)
bismark.data <- importBismark(file, chrom.lengths=arabidopsis_chromosomes)

## Get an example file in BSMAP format
file <- system.file("extdata","arabidopsis_BSMAP.txt", package="methimpute")
data(arabidopsis_chromosomes)
bsmap.data <- importBSMAP(file, chrom.lengths=arabidopsis_chromosomes)

## Get an example file in Methylpy format
file <- system.file("extdata","arabidopsis_methylpy.txt", package="methimpute")
data(arabidopsis_chromosomes)
arabidopsis_chromosomes$chromosome <- sub('chr', '', arabidopsis_chromosomes$chromosome)
methylpy.data <- importMethylpy(file, chrom.lengths=arabidopsis_chromosomes)

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