An R package for the creation of complex genomic profile plots

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Documentation for package ‘recoup’ version 1.26.0

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

Help Pages

buildAnnotationDatabase	Build a local annotation database for recoup
buildAnnotationStore	Build a local annotation database for recoup
buildCustomAnnotation	Import custom annotation to the recoup annotation database from GTF file
calcCoverage	Calculate coverages over a genomic region
coverageRef	Calculate coverage in a set of reference genomic regions (ChIP-Seq or unspliced mode)
coverageRnaRef	Calculate coverage in a set of reference genomic regions (RNA-Seq or spliced mode)
getAnnotation	Annotation downloader
getBiotypes	List default Ensembl biotypes
getInstalledAnnotations	Load a recoup annotation element
getr	Get and set some reusable objects from a recoup object
importCustomAnnotation	Import a recoup custom annotation element
kmeansDesign	Apply k-means clustering to profile data
loadAnnotation	Load a recoup annotation element
mergeRuns	Merge recoup outputs of same type
preprocessRanges	Read and preprocess BAM/BED files to GRanges
profileMatrix	Calculate final profile matrices for plotting
recoup	Create genomic signal profiles in predefined or custom areas using short sequence reads
recoup-defunct	Defunct functions in package 'recoup'
recoup-deprecated	Deprecated functions in package 'recoup'
recoupCorrelation	Plot (faceted) average genomic coverage correlations
recoupHeatmap	Plot genomic coverage heatmaps
recoupPlot	Plot list objects returned by recoup
recoupProfile	Plot (faceted) average genomic coverage profiles
recoup_test_data	Reference and genomic sample regions for recoup testing
removeData	Remove data from recoup list object
rpMatrix	Reads per million profile matrices for plotting
setr	Get and set some reusable objects from a recoup object
sliceObj	Subset recoup output list objects
test.design	Reference and genomic sample regions for recoup testing
test.exons	Reference and genomic sample regions for recoup testing
test.genome	Reference and genomic sample regions for recoup testing
test.input	Reference and genomic sample regions for recoup testing