Additional functions for working with ChIP-Seq data

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Documentation for package ‘extraChIPs’ version 1.10.0

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

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