addHbond: Class '"hbond"': Provides data and functions for calculation...

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

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)

wokai/spliceSites documentation built on May 4, 2019, 9:46 a.m.