# Estimate Promoter Activity from RNA-Seq data

## Documentation for package ‘proActiv’ version 1.19.3

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

## Help Pages

'intronRanges<-'-method | S4 class for promoter annotation data for a specific annotation version
'promoterCoordinates<-'-method | S4 class for promoter annotation data for a specific annotation version
'promoterIdMapping<-'-method | S4 class for promoter annotation data for a specific annotation version
boxplotPromoters | Visualizes promoter activity and gene expression with boxplots
calculateJunctionReadCounts | Calculate the total number of junction reads overlapping with the introns of each promoter for the input junction file
calculatePromoterReadCounts | Calculate the promoter read counts using junction read counts approach for all the input junction files
getAbsolutePromoterActivity | Prepare the absolute promoter activity table including the promoter and gene ids
getAlternativePromoters | Identifies alternative promoters.
getGeneExpression | Prepare the gene expression table including the gene ids
getRelativePromoterActivity | Prepare the relative promoter activity table including the promoter and gene ids
integrateProactiv | Integrate multiple proActiv runs
intronRanges | S4 class for promoter annotation data for a specific annotation version
intronRanges-method | S4 class for promoter annotation data for a specific annotation version
intronRanges<- | S4 class for promoter annotation data for a specific annotation version
intronRanges<--method | S4 class for promoter annotation data for a specific annotation version
normalizePromoterReadCounts | Normalize promoter read counts using DESeq2
plotHeatmap | Visualizes heatmap of features for samples
plotPCA | Performs principal component analysis
preparePromoterAnnotation | Prepares promoter annotation from a gtf or txdb
proActiv | Estimates promoter counts and activity in a single command
PromoterAnnotation | S4 class for promoter annotation data for a specific annotation version
PromoterAnnotation-class | S4 class for promoter annotation data for a specific annotation version
promoterAnnotation.gencode.v34.subset | Promoter annotation for Gencode.v34 (subset)
promoterCoordinates | S4 class for promoter annotation data for a specific annotation version
promoterCoordinates-method | S4 class for promoter annotation data for a specific annotation version
promoterCoordinates<- | S4 class for promoter annotation data for a specific annotation version
promoterCoordinates<--method | S4 class for promoter annotation data for a specific annotation version
promoterIdMapping | S4 class for promoter annotation data for a specific annotation version
promoterIdMapping-method | S4 class for promoter annotation data for a specific annotation version
promoterIdMapping<- | S4 class for promoter annotation data for a specific annotation version
promoterIdMapping<--method | S4 class for promoter annotation data for a specific annotation version