annotation {spliceSites} | R Documentation

## Annotation functions for `gapSites` objects

### Description

The `annotate` function takes a `gapSites` and a `refGenome` object and returns a list which additionally contains a 'class' attribute 'annotationResult'. The object is intended as input for the `annotation` member function of class `gapSites`. The `annotation` member functions act as writing and reading accessor for annotation data inside `gapSites` objects.

### Usage

    annotate(object, junc)

### Arguments

`object` | [gapSites]. Align-gap data for which annotations are provided via overlap.

`junc` | [refJunctions]. Object which provides annotated splice site positions.

### Details

The `annotation` reading accessor takes a `gapSites` object and returns a `annAlignGaps` object. The `annotation` writing accessor takes a `gapSites` and a `annotationResult` object and copies the contained table into the `annotation` slot of the `gapSites` object.

### Value

annAlignGaps

### Author(s)

Wolfgang Kaisers

### Examples

    # A) Create gapSites object
    bam <- system.file("extdata", "rna_fem.bam", package="spliceSites")
    reader <- bamReader(bam[1], idx=TRUE)
    ga <- alignGapList(reader)
    bamClose(reader)

    # B) Read refGenome object
    ucf <- system.file("extdata", "uc_small_junc.RData", package="spliceSites")
    ucj <- loadGenome(ucf)

    # C) Add annotation data
    annotation(ga) <- annotate(ga, ucj)

[Package spliceSites version 1.31.0 Index]