subset_methrix {methrix} | R Documentation

## Subsets `methrix` object based on given conditions.

### Description

Subsets `methrix` object based on given conditions.

### Usage

    subset_methrix(
      m,
      regions = NULL,
      contigs = NULL,
      samples = NULL,
      overlap_type = "within"
    )

### Arguments

`m` | `methrix` object
`regions` | genomic regions to subset by. Could be a data.table with 3 columns (chr, start, end) or a `GenomicRanges` object
`contigs` | chromosome names to subset by
`samples` | sample names to subset by
`overlap_type` | defines the type of the overlap of the CpG sites with the target region. Default value is 'within'. For detailed description, see the `foverlaps` function of the `data.table` package.

### Details

Takes `methrix` object and filters CpGs based on coverage statistics

### Value

An object of class `methrix`

### Examples

    data('methrix_data')
    #Subset to chromosome 1
    subset_methrix(methrix_data, contigs = 'chr21')

[Package methrix version 1.4.07 Index]