addGenomeData-ExpressionSet {spliceSites} | R Documentation

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

### Description

The function takes an ExpressionSet object generated by `readExpSet`, annotates featureData and adds MaxEnt-scores, Exon-Intron sequences to featureData slot.

### Usage

        addGenomeData(object, dna, junc)

### Arguments

`object` | ExpressionSet object generated by readExpSet.
`dna` | DNAStringSet containing genomic sequence.
`junc` | refJunctions

### Details

The function adds new columns to `featureData` as described in `varMetadata`. The ljseq and rjseq columns contain exon-intron junction sequence (from xJunc, dnaRanges using featlen=3, gaplen=8). The ldin and rdin columns contain first intronic dinucleotides from left and right gap-site border.

### Value

ExpressionSet

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

    # E) Add Genome data
    dnafile<-system.file("extdata","dna_small.RData",package="spliceSites")
    load(dnafile)
    esg <- addGenomeData(es, dna_small, juc)

[Package spliceSites version 1.28.0 Index]