import {methimpute} | R Documentation

## Methimpute data import

### 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)

[Package methimpute version 1.6.0 Index]