# An R package for the creation of complex genomic profile plots

## Documentation for package ‘recoup’ version 1.39.2

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

## Help Pages

buildAnnotationDatabase | 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
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