# Additional functions for working with ChIP-Seq data

## Documentation for package ‘extraChIPs’ version 1.16.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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