annotate-ExpressionSet {spliceSites} | R Documentation

## Adds annotation data to existing ExpressionSet (created by `readExpSet`)

### Description

Reads `featureData` from incoming Expression set which should contain range data on embedding exons for gap-sites. The annotate function then overlaps the ranges with given annotation data. The result of overlapping is written into a AnnotatedDataFrame.

### Arguments

`object` | ExpressionSet
`genome` | refGenome

### Value

AnnotatedDataFrame

### Author(s)

Wolfgang Kaisers

### Examples

    # A) Names of BAM-files
    bam <- character(2)
    bam[1] <- system.file("extdata", "rna_fem.bam", package="spliceSites")
    bam[2] <- system.file("extdata", "rna_mal.bam", package="spliceSites")

    # B) Experiment Profile
    prof <- data.frame(gender=c("f", "m"))
    meta <- data.frame(labelDescription=names(prof), row.names=names(prof))
    pd<-new("AnnotatedDataFrame", data=prof, varMetadata=meta)

    # C) Read ExpressionSet
    es <- readExpSet(bam, phenoData=pd)

    # D) Annotate ExpressionSet
    ucf <- system.file("extdata", "uc_small.RData", package="spliceSites")
    uc <- loadGenome(ucf)
    juc <- getSpliceTable(uc)
    ann <- annotate(es, juc)

[Package spliceSites version 1.28.0 Index]