getCisGroups: getCisGroups

Description Usage Arguments Value Methods (by class) Author(s) Examples

Description

Function for grouping peaks based on proximity along chromosomes

Usage

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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)

Author(s)

Alicia Schep

Examples

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# 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. 1, 2018, 3:47 a.m.