addHbond {spliceSites} | R Documentation

## Class `"hbond"`: Provides data and functions for calculation of HBond scores for 5' splice-sites.

### Description

The `addHbond` methods add HBond scores to `gapSites` and `cdRanges` objects. HBond scores provide a measure for the capability of a 5' splice-site to form H-bonds with the U1 snRNA. The function requires at least 3 exon nucleotides and 8 intron nucleotides. The first two intron nucleotides are expected to be 'GT' (for other values the returned score will be 0). The routine equally accepts upper and lower case characters.

### Usage

    addHbond(x,dna)

### Arguments

`x` | `gapSites`. The object to which HBond scores are added.

`dna` | `DNAStringSet`. Reference sequence identifier.

### Details

In `cdRanges` objects, the function adds a `hbond` column. In `gapSites` objects, the function adds a `lhbond` (left side) and a `rhbond` (right side) column. The `lhbond` values always assume '+'-strand (because HBond works on the 5' side). The `rhbond` values always assume '-'-strand. Therefore, there will be discrepancies in the output of `write.annDNA.tables` because the `leftseq` and `rightseq` sequences are reverse-complemented according to the `strand` column: The xhbond may be > 0 without GT at position 4 (but with AC at position 7).

### Author(s)

Wolfgang Kaisers

### References

http://www.uni-duesseldorf.de/rna/html/hbond_score.php

### 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) HBond
    gab<-addHbond(ga,dna_small)

    # D) cdRanges
    lj<-lJunc(ga,featlen=3,gaplen=8,strand='+')
    ljd<-dnaRanges(lj,dna_small)
    ljdh<-addHbond(ljd)

[Package spliceSites version 1.28.0 Index]