PromoterAnnotation-class: S4 class for promoter annotation data for a specific...

In GoekeLab/proActiv: Estimate Promoter Activity from RNA-Seq data

Description

S4 class for promoter annotation data for a specific annotation version

Usage

PromoterAnnotation(
  intronRanges = GenomicRanges::GRanges(),
  promoterIdMapping = data.frame(),
  promoterCoordinates = GenomicRanges::GRanges()
)

intronRanges(x)

## S4 method for signature 'PromoterAnnotation'
intronRanges(x)

promoterIdMapping(x)

## S4 method for signature 'PromoterAnnotation'
promoterIdMapping(x)

promoterCoordinates(x)

## S4 method for signature 'PromoterAnnotation'
promoterCoordinates(x)

intronRanges(x) <- value

## S4 replacement method for signature 'PromoterAnnotation'
intronRanges(x) <- value

promoterIdMapping(x) <- value

## S4 replacement method for signature 'PromoterAnnotation'
promoterIdMapping(x) <- value

promoterCoordinates(x) <- value

## S4 replacement method for signature 'PromoterAnnotation'
promoterCoordinates(x) <- value

Arguments

intronRanges	A GRanges object containing annotated intron ranges
promoterIdMapping	A data.frame containing mapping between transcript, TSS, promoter and gene ids
promoterCoordinates	A GRanges object containing promoter coordinates
x	A PromoterAnnotation object
value	intronRanges, promoterIdMapping or promoterCoordinates to be assigned

Value

A promoter annotation object with three slots: intronRanges, promoterIdMapping and promoter Coordinates

Functions

• intronRanges: Getter for intronRanges

• intronRanges,PromoterAnnotation-method: Getter for intronRanges

• promoterIdMapping: Getter for promoterIdMapping

• promoterIdMapping,PromoterAnnotation-method: Getter for promoterIdMapping

• promoterCoordinates: Getter for promoterCoordinates

• promoterCoordinates,PromoterAnnotation-method: Getter for promoterCoordinates

• intronRanges<-: Setter for intronRanges

• intronRanges<-,PromoterAnnotation-method: Setter for intronRanges

• promoterIdMapping<-: Setter for promoterIdMapping

• promoterIdMapping<-,PromoterAnnotation-method: Setter for promoterIdMapping

• promoterCoordinates<-: Setter for promoterCoordinates

• promoterCoordinates<-,PromoterAnnotation-method: Setter for promoterCoordinates

Slots

intronRanges

A GRanges object. The intron ranges annotated with the promoter information.

promoterIdMapping

A data.frame object. The id mapping between transcript ids, names, TSS ids, promoter ids and gene ids.

promoterCoordinates

A GRanges object. Promoter coordinates (TSS) with gene id and internal promoter state

Examples

promoterAnnotation <- PromoterAnnotation()
intronRanges(promoterAnnotation) <- intronRanges(
                                    promoterAnnotation.gencode.v34.subset)
promoterIdMapping(promoterAnnotation) <- promoterIdMapping(
                                    promoterAnnotation.gencode.v34.subset)
promoterCoordinates(promoterAnnotation) <- promoterCoordinates(
                                    promoterAnnotation.gencode.v34.subset)

GoekeLab/proActiv documentation built on Jan. 30, 2022, 3:52 a.m.