hbond-class: Class '"hbond"'

In spliceSites: A bioconductor package for exploration of alignment gap positions from RNA-seq data

Description

Provides methods and data for calculation of HBond 5'splice-site scores. 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 hbond function takes a vector DNA sequences and a vector of position (pos) values. The position values represent the 1-based position of the last exon nucleotide. Therefore all position values must be >=3 and the sequence length must be >= pos+8.

Details

The first two intron nucleotides must be 'GT' otherwise returned value is 0. All other sequence characters must be in "ATCG" (capitalization does not matter). When any other character (such as N) is found, the function also returns 0.

Creation of hbond objects

Objects can be created by load.hbond().

Slots

ev:

Object of class "environment" Contains external score data.

basedir:

Object of class "character" Directory from which external data is restored.

Methods

basedir

signature(x = "hbond"): Returns basedir value.

basedir<-

signature(x = "hbond",value="character"): Sets basedir value.

hbond

signature(x = "hbond",seq="character",pos="integer"): Calculates score5 value for seq at given position.

Author(s)

Wolfgang Kaisers

References

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

Examples

hb<-load.hbond()
seq<-c("CAGGTGAGTTC","ATGCTGGAGAA","AGGGTGCGGGC","AAGGTAACGTC","AAGGTGAGTTC")
hbond(hb,seq,3)

spliceSites documentation built on May 6, 2019, 3:05 a.m.