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

Description Usage Arguments Value Functions Slots Examples

Description

S4 class for promoter annotation data for a specific annotation version

Usage

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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

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

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GoekeLab/proActiv documentation built on June 26, 2021, 6:39 a.m.