getCisGroups: getCisGroups

In chromVAR: Chromatin Variation Across Regions

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)

chromVAR documentation built on Nov. 8, 2020, 6:46 p.m.