addGenomeData-gapSites {spliceSites} | R Documentation

## Add MaxEnt-scores, Exon-Intron junction sequences score to Feature Data in `gapSites` object.

### Description

The function takes an gapSites object, adds annotation data, MaxEnt-scores, Exon-Intron sequences to featureData slot.

### Arguments

`object` | gapSites object
`dna` | DNAStringSet containing genomic sequence.
`junc` | refJunctions

### Details

The function adds new columns to `featureData` as described in `varMetadata`.

### Value

gapSites

### Author(s)

Wolfgang Kaisers

### Examples

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

    # B) Load DNA
    dnafile <- system.file("extdata", "dna_small.RData", package="spliceSites")
    load(dnafile)

    # C) maxEnt
    mes<-load.maxEnt()
    gae<-addMaxEnt(ga,dna_small,mes)
    getMeStrand(gae)
    sae<-setMeStrand(gae)

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

    esg <- addGenomeData(ga, dna_small, juc)

[Package spliceSites version 1.28.0 Index]