PromoterAnnotation-class {proActiv} | R Documentation |
S4 class for promoter annotation data for a specific annotation version
PromoterAnnotation( intronRanges = GRanges(), promoterIdMapping = data.frame(), promoterCoordinates = 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
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 |
A promoter annotation object with three slots: intronRanges, promoterIdMapping and promoter Coordinates
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
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
promoterAnnotation <- PromoterAnnotation() intronRanges(promoterAnnotation) <- intronRanges( promoterAnnotation.gencode.v34.subset) promoterIdMapping(promoterAnnotation) <- promoterIdMapping( promoterAnnotation.gencode.v34.subset) promoterCoordinates(promoterAnnotation) <- promoterCoordinates( promoterAnnotation.gencode.v34.subset)