uniqueJuncAnn {spliceSites} | R Documentation

## uniqueJuncAnn method for ExpressionSet

### Description

uniqueJuncAnns adds annotation data to ExpressionSet and removes not-matching sites.

### Usage

    uniqueJuncAnn(object,junc,ann=TRUE,...)

### Arguments

`object` | `ExpressionSet`. Object containing gap-site expression data.
`junc` | `refJunctions`. Object containing splice-junction sites.
`ann` | `logical`. Default: `TRUE`. When `TRUE` the unannotated sites are removed, otherwise the annotated sites are removed.
`...` | Unused.

### Value

ExpresssionSet

### 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)
    ucj<-getSpliceTable(uc)

    # E) Extract unique annotated junction sites.
    uja<-uniqueJuncAnn(es,ucj)

[Package spliceSites version 1.28.0 Index]