coverage_filter {methrix} | R Documentation

## Filter matrices by coverage

### Description

Filter matrices by coverage

### Usage

    coverage_filter(
      m,
      cov_thr = 1,
      min_samples = 1,
      prop_samples = 0,
      group = NULL,
      n_chunks = 1,
      n_cores = 1
    )

### Arguments

`m` | `methrix` object
`cov_thr` | minimum coverage required to call a loci covered
`min_samples` | Minimum number of samples that should have a loci with coverage >= `cov_thr`. If `group` is given, then this applies per group. Only need one of `prop_samples` or `min_samples`.
`prop_samples` | Minimum proportion of samples that should have a loci with coverage >= `cov_thr`. If `group` is given, then this applies per group. Only need one of `prop_samples` or `min_samples`.
`group` | a column name from sample annotation that defines groups. In this case, the number of min_samples will be tested group-wise.
`n_chunks` | Number of chunks to split the `methrix` object in case it is very large. Default = 1.
`n_cores` | Number of parallel instances. `n_cores` should be less than or equal to `n_chunks`. If `n_chunks` is not specified, then `n_chunks` is initialized to be equal to `n_cores`. Default = 1.

### Details

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

### Value

An object of class `methrix`

### Examples

    data('methrix_data')
    #keep only CpGs which are covered by at-least 1 read across 3 samples
    coverage_filter(m = methrix_data, cov_thr = 1, min_samples = 3)

[Package methrix version 1.4.07 Index]