annotation: Annotation functions for 'gapSites' objects

In spliceSites: A bioconductor package for exploration of alignment gap positions from RNA-seq data

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)

spliceSites documentation built on May 6, 2019, 3:05 a.m.