getCisGroups {chromVAR} | R Documentation

## getCisGroups

### Description

Function for grouping peaks based on proximity along chromosomes

### Usage

    getCisGroups(object, ...)

    ## S4 method for signature 'RangedSummarizedExperiment'
    getCisGroups(object, grpsize = 25,
      stepsize = 10)

    ## S4 method for signature 'GenomicRanges'
    getCisGroups(object, grpsize = 25, stepsize = 10)

### Arguments

`object` | GenomicRanges or RangedSummarizedExperiment
`...` | additional arguments
`grpsize` | number of peaks to include in each grouop
`stepsize` | number of peaks between each new set of groups

### Value

SummarizedExperiment with annotationMatches assay storing which peaks belong to which groups

### Methods (by class)

- `RangedSummarizedExperiment`: method for RangedSummarizedExperiment

- `GenomicRanges`: method for GenomicRanges

### Author(s)

Alicia Schep

### Examples

    # Load very small example counts (already filtered)
    data(mini_counts, package = "chromVAR")
    mini_counts <- sort(mini_counts)
    cisg <- getCisGroups(mini_counts)

[Package chromVAR version 1.2.0 Index]