addMaxEnt {spliceSites} | R Documentation

## addMaxEnt: Extract subset of data contained in given range given object.

### Description

addMaxEnt adds new columns to object data which contain MaxEnt-Score derived values. `mxe_ps5` contains `score5` values for left align-gap (exon-intron) boundary (i.e. assumed to reside on '+'-strand. `mxe_ps3` contains `score3` (maxent) values for right align-gap (intron-exon) boundary (i.e. assumed to reside on '+'-strand). `mxe_ms5` contains `score5` values for right align-gap (exon-intron) boundary on `reverseComplement` transformed sequence (i.e. assumed to reside on '-'-strand). `mxe_ms3` contains `score3` values for left align-gap (intron-exon) boundary on `reverseComplement` transformed sequence (i.e. assumed to reside on '-'-strand). From these values, `s3strand`, `s5strand` and `meStrand` are derived: `s3strand` is '+' when `mxe_ps5` >= `mxe_ms5` and '-' otherwise; `s3strand` is '+' when `mxe_ps3` >= `mxe_ms3` and '-' otherwise. `meStrand` equals `s5strand` when `s5strand`=`s3strand` and '*' otherwise. The function `setMeStrand` copies existing `meStrand` values into `strand` column (and throws an error when `meStrand` does not exist).

### Usage

    addMaxEnt(x,dna,maxent,digits=1)

### Arguments

`x` | gapSites.

`dna` | DNAStringSet. Reference sequence identifier.

`maxent` | maxEnt. Contains score table which are internally used by `score3` and `score5` methods.

`digits` | Numeric. Default value: 1. Internally calculated maxent scores are rounded to given number of decimal places.

### 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)

[Package spliceSites version 1.28.0 Index]