Package index • extraChIPs

Overview
Range-Based Operations
`makeConsensus()`	Make a set of consensus peaks
`mapGrlCols()`	Collapse a GRangesList adding multiple columns from each element
`chopMC()`	Keep unique ranges and collapse mcols
`distinctMC()`	Keep distinct ranges and mcols
`reduceMC()`	Reduce ranges retaining mcols
`setdiffMC()` `intersectMC()` `unionMC()`	Perform set operations retaining mcols
`bestOverlap()`	Find the best overlap between GRanges
`propOverlap()`	Find the proportions of an overlapping range
`colToRanges()`	Coerce a column to a GRanges object
`defineRegions()`	Define Genomic Regions Based on Gene Annotations
`partitionRanges()`	Partition a set of Genomic Ranges
`stitchRanges()`	Stitch Ranges within a given distance
Functions For Differential Signal Analysis
`dualFilter()`	Apply two filters to sliding windows
`centrePeaks()`	Re-estimate peak centres from coverage
`importPeaks()`	Import peaks
`fitAssayDiff()`	Detect Differential ChIP Signal
`getProfileData()`	Get Profile Data surrounding specified ranges
`grlToSE()`	Set columns from a GRangesList as Assays in a SummarizedExperiment
`mapByFeature()`	Map Genomic Ranges to genes using defined features
`mergeByCol()`	Merge sliding windows using a specified column
`mergeByHMP()`	Merge Sliding Windows using the Harmonic Mean P
`mergeBySig()`	Merge overlapping ranges based on p-values
`voomWeightsFromCPM()`	Estimate voom precision weights directly From CPM values
Visualisation
`plotAssayDensities()`	Plot Densities for any assay within a SummarizedExperiment
`plotAssayHeatmap()`	Draw a heatmap from a single SummarizedExperiment assay
`plotAssayPCA()`	Plot PCA For any assay within a SummarizedExperiment
`plotAssayRle()`	Plot RLE for a given assay within a SummarizedExperiment
`plotGrlCol()`	Draw a plot from a GRangesList column
`plotHFGC()`	Plot a Genomic Region showing HiC, Features, Genes and Coverage
`plotOverlaps()`	Plot Overlaps Between List Elements
`plotPairwise()`	Plot Pairwise Values from a GRangeList
`plotPie()`	Draw Pie Graphs based on one or more columns
`plotProfileHeatmap()`	Draw a coverage Profile Heatmap
`plotSplitDonut()`	Draw Two-Level Donut Charts
Coercion & Convenience Functions
`addDiffStatus()`	Add a status column
`as_tibble(<DataFrame>)` `as_tibble(<GenomicRanges>)` `as_tibble(<Seqinfo>)` `as_tibble(<GInteractions>)` `as_tibble(<SummarizedExperiment>)` `as_tibble(<TopTags>)`	Convert to a tibble
`collapseGenes()`	Collapse a vector of gene names
`defineSeqinfo()`	Use package data to define a Seqinfo object
Data Objects
`grch37.cytobands` `grch38.cytobands`	Cytogenetic bands
`ex_trans` `ex_genes` `ex_prom` `ex_hic`	Datasets for an example region
`se` `peaks`	Datasets for the Fixed-Width Vignette

Reference

Overview

Range-Based Operations

Functions For Differential Signal Analysis

Visualisation

Coercion & Convenience Functions

Data Objects