annGapSites-class {spliceSites} | R Documentation

## Class `"annGapSites"`

### Description

Contains data from align gaps together with annotation data (and optional data about alternative splice positions). Objects of this clasa are returned from the `annotation` member function for class `gapSites`.

### Details

`plot_diff` plots tabled distance between inner gap-site border and annotated exon-intron boundaries.

### Objects from the Class

Objects can be created by calls of the form `annotation` on `gapSites` objects.

### Slots

`nAligns`:

  Object of class `"numeric"` Total number of aligns.

`nAlignGaps`:

  Object of class `"numeric"` Total number of gapped aligns.

`dt`:

  `"data.frame"`. Contains gap-positions, annotation data and optional alternative position data.

`annotation`:

  `"data.frame"`. Contains annotation data.

`profile`:

  `"data.frame"`. Contains descriptive data for source probes (BAM-files).

### Extends

Class `"gapSites"`, directly.

### Methods

as.data.frame

  `signature(x = "annGapSites")`: Returns the contained data.

### Author(s)

Wolfgang Kaisers

### Examples

    # A) Read gapSites from BAM
    bam <- system.file("extdata", "rna_fem.bam", package="spliceSites")
    reader <- bamReader(bam, idx=TRUE)
    ga <- alignGapList(reader)
    bamClose(reader)

    # B) Load annotation data
    ucf <- system.file("extdata", "uc_small_junc.RData", package="spliceSites")
    ucj <- loadGenome(ucf)

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

    # D) Retrieve annotation
    aga <- annotation(ga)
    aga

    # D) plot_diff
    aga <- annotation(ga)
    plot_diff(aga)

[Package spliceSites version 1.28.0 Index]