addHbond {spliceSites} | R Documentation |
"hbond"
: Provides data and functions for calculation of
HBond scores for 5' splice-sites.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.
addHbond(x,dna)
x |
|
dna |
|
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).
Wolfgang Kaisers
http://www.uni-duesseldorf.de/rna/html/hbond_score.php
# 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)