getCisGroups {chromVAR} | R Documentation |
Function for grouping peaks based on proximity along chromosomes
getCisGroups(object, ...) ## S4 method for signature 'RangedSummarizedExperiment' getCisGroups(object, grpsize = 25, stepsize = 10) ## S4 method for signature 'GenomicRanges' getCisGroups(object, grpsize = 25, stepsize = 10)
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 |
SummarizedExperiment with annotationMatches assay storing which peaks belong to which groups
RangedSummarizedExperiment
: method for RangedSummarizedExperiment
GenomicRanges
: method for GenomicRanges
Alicia Schep
# Load very small example counts (already filtered) data(mini_counts, package = "chromVAR") mini_counts <- sort(mini_counts) cisg <- getCisGroups(mini_counts)