write_bedgraphs {methrix} | R Documentation

## Writes bedGraphs from methrix object

### Description

Writes bedGraphs from methrix object

### Usage

    write_bedgraphs(
      m,
      output_dir = NULL,
      rm_NA = TRUE,
      force = FALSE,
      n_thr = 4,
      compress = TRUE,
      SeqStyle = "UCSC",
      multiBed = NULL,
      metilene = FALSE,
      phenoCol = NULL
    )

### Arguments

`m` | `methrix` object
`output_dir` | Output directory name where the files should be saved. If `NULL` creats a `tempdir`
`rm_NA` | remove NAs
`force` | forces to create files if they are existing
`n_thr` | Default 4.
`compress` | Whether to compress the output. Default TRUE
`SeqStyle` | Default 'UCSC' with 'chr' prefix.
`multiBed` | Default NULL. If provided a filename, a single bedGraph file with all samples included is generated.
`metilene` | Default FALSE. If TRUE outputs bedgraphs in 'metilene' format that can be directly used for DMR calling with 'metilene'. This option works only when `multiBed = TRUE`.
`phenoCol` | Default NULL. 'condition' column from colData. Only applicable if `metilene = TRUE`

### Value

writes bedgraph files to output

### Examples

    data('methrix_data')
    write_bedgraphs(m = methrix_data, output_dir = './temp')
    #Export to metline format for DMR calling with metline
    write_bedgraphs(m = methrix_data, output_dir = "./temp", rm_NA = FALSE, metilene = TRUE,multiBed = "metline_ip", phenoCol = "Condition")

[Package methrix version 1.4.07 Index]