getCisGroups

Function for grouping peaks based on proximity along chromosomes

getCisGroups(object, ...)

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

# S4 method for 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

Examples

# NOT RUN {
# Load very small example counts (already filtered)
data(mini_counts, package = "chromVAR")
mini_counts <- sort(mini_counts)
cisg <- getCisGroups(mini_counts)
# }