PromoterAnnotation-class {proActiv} | R Documentation

## S4 class for promoter annotation data for a specific annotation version

### 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)

[Package proActiv version 1.4.0 Index]