S4 class for promoter annotation data for a specific annotation version

Source: R/PromoterAnnotation-class.R

S4 class for promoter annotation data for a specific annotation version

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

intronRanges(x)

# S4 method for PromoterAnnotation
intronRanges(x)

promoterIdMapping(x)

# S4 method for PromoterAnnotation
promoterIdMapping(x)

promoterCoordinates(x)

# S4 method for PromoterAnnotation
promoterCoordinates(x)

intronRanges(x) <- value

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

promoterIdMapping(x) <- value

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

promoterCoordinates(x) <- value

# S4 method for 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)