extraChIPs-package: extraChIPs: A package for enabling and extending ChIP-Seq...

In steveped/chipExtra: Additional functions for working with ChIP-Seq data

extraChIPs: A package for enabling and extending ChIP-Seq analysis

Description

The package provides three categories of important functions: Range-based, Visualisation and Convenience functions, with most centred around GenomicRanges objects

Range-based Functions

Many of the range-based functions included in this package have a focus on retaining the mcols information whilst manipulating the ranges, such as reduceMC() which not only reduces the Ranges, but collapses the mcols into vectors or IRanges::CompressedList objects. Key function from this group are:

• reduceMC(), setdiffMC(), intersectMC(), unionMC(), distinctMC() and chopMC()

• bestOverlap() and propOverlap() provide simple output easily able to be added as a column within the mcols element

• as_tibble() coerces a GRanges object to a tibble::tibble.

• colToRanges() enables parsing of a single column to a GRanges object, setting all other columns as the mcols element.

• stitchRanges() merges nearby ranges setting barrier ranges which cannot be crossed when merging

• partitionRanges() break apart one set of ranges by another

• dualFilter() filters ranges from sliding windows using a guide set of reference ranges where signal is confidently expected

• mergeByCol() merges overlapping ranges, as produced by sliding windows

• mapByFeature() is able to map a set of GRanges to the most appropriate gene, using any optional combination of promoters, enhancers and HiC interactions

• grlToSE() takes selected columns from a GRangesList and sets them as assays within a SummarizedExperiment::RangedSummarizedExperiment object. Used for combining peak intensities or results across multiple ChIP targets.

Visualisation Functions

• plotHFGC() is a wrapper to Gviz plotting functions, able to take any combination of HiC, Features, Genes and Coverage (i.e. BigWig) and plot a specified range.

• plotOverlaps() visualises overlapping ranges as an UpSet plot or Venn Diagram

• plotProfileHeatmap() plots the average signal around a set of ranges, as prepared by getProfileData()

• plotPie() and plotSplitDonut() enable simple comparison across multiple annotation columns within a GRanges object.

• plotAssayDensities(), plotAssayPCA() and plotAssayRle() provide simple interfaces to plotting key values from a SummarizedExperiment::RangedSummarizedExperiment.

Convenience Functions

• fitAssayDiff() enables differential signal analysis on a SummarizedExperiment object

• collapseGenes() prints a vector of genes for an rmarkdown document, using italics.

• importPeaks() imports large numbers of broadPeak or narrowPeak files

• makeConsensus() forms consensus peaks from overlapping ranges within a GRangesList()

• voomWeightsFromCPM() allows creation of an limma::EList object as would be created from counts by limma::voom(), but using edgeR::cpm() values as input.

Author(s)

Stevie Pederson

See Also

Useful links:

• https://github.com/smped/extraChIPs

• Report bugs at https://github.com/smped/extraChIPs/issues

steveped/chipExtra documentation built on Aug. 1, 2024, 12:33 a.m.