shapiroDonor: shapiroDonor
In SPLINTER: Splice Interpreter of Transcripts

Description Usage Arguments Value Author(s) See Also Examples

Shapiro and Senapathy (1987) have developed a method to score the strength of a splice site based on percentages of each nucleotide at each position. Shapiro's score of donor site (range is from -3 [exon] to +7 [intron]) is : 100 * (t - min)/ (max - min), where t is the sum of percentages at positions -3 to +7, min is the sum of the lowest percentages at positions -3 to +7, and max is the sum of the highest percentages at positions -3 to +7.

1	shapiroDonor(reference_fasta, target_fasta)

`reference_fasta`	vector of strings or DNAStringSet of reference splice list
`target_fasta`	vector of strings or DNAStringSet of fasta to score

data.frame with Shapiro scores

Diana Low

http://www.softberry.com/spldb/SpliceDB.html

library(BSgenome.Mmusculus.UCSC.mm9)
bsgenome <- BSgenome.Mmusculus.UCSC.mm9
data_path<-system.file("extdata",package="SPLINTER")
splice_data<-extractSpliceEvents(data=paste(data_path,"/skipped_exons.txt",sep=""))
splice_sites<-extractSpliceSites(splice_data)
donor.ss<-getSeq(bsgenome,splice_sites)
##sdonor<-shapiroDonor(donor.m,donor.ss)