subsetByLoci {minfi} | R Documentation

## Subset an RGChannelset by CpG loci.

### Description

Subset an RGChannelSet by CpG loci.

### Usage

    subsetByLoci(rgSet, includeLoci = NULL, excludeLoci = NULL,
                 keepControls = TRUE, keepSnps = TRUE)

### Arguments

`rgSet` | An object of class `RGChannelSet` (or `RGChannelSetExtended`).
`includeLoci` | A character vector of CpG identifiers which should be kept.
`excludeLoci` | A character vector of CpG identifiers which should be excluded.
`keepControls` | Should control probes be kept?
`keepSnps` | Should SNP probes be kept?

### Details

This task is non-trivial because an `RGChannelSet` is indexed by probe position on the array, not by loci name.

### Value

An object of class `RGChannelSet`, which some probes removed.

### Examples

    if(require(minfiData)) {
      loci <- c("cg00050873", "cg00212031", "cg00213748", "cg00214611")
      subsetByLoci(RGsetEx.sub, includeLoci = loci)
      subsetByLoci(RGsetEx.sub, excludeLoci = loci)
    }

[Package minfi version 1.38.0 Index]