The R package to curate and merge enriched genomic regions into consensus peak sets

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Documentation for package ‘peakCombiner’ version 0.99.602

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

centerExpandRegions	Modifies genomic regions by centering and then expanding them
checkDataStructure	Control structure of peakCombiner data structure
collapseSummits	collapse_summits
combineRegions	Combine overlapping genomic regions from different samples to create a single set of consensus genomic regions
crAddSummit	Update the center and score information
crDisjoinFilter	Separate genomic regions by coverage (disjoin) and filter input regions
crOverlapWithSummits	Overlap genomic regions with original summits to remove false positive
crReduce	Recombine (reduce) input regions
defineExpansion	Calculate expansion value from median input region size
filterRegions	Apply user-defined filtering options to genomic regions.
prepareInputRegions	Prepare input data for peakCombiner package
syn_blacklist	Synthetic file with blacklisted regions for peakCombiner
syn_control_rep1_narrowPeak	Synthetic data set for control rep 1 sample in narrowPeak file format
syn_data_bed	Synthetic data set of genomic coordinates and meta data columns
syn_data_control01	Synthetic data set of genomic coordinates and meta data columns filtered for control rep 1 sample
syn_data_granges	Synthetic data set of genomic coordinates and meta data columns
syn_data_tibble	Synthetic data set of genomic coordinates and meta data columns as tibble
syn_data_treatment01	Synthetic data set of genomic coordinates and meta data columns filtered for treatment rep 1 sample
syn_sample_sheet	Synthetic sample sheet to load example data with peakCombiner
syn_treatment_rep1_narrowPeak	Synthetic data set for treatment rep 1 sample in narrowPeak file format