shapiroAcceptor: shapiroAcceptor
In SPLINTER: Splice Interpreter of Transcripts

Description Usage Arguments Value Author(s) See Also Examples

Shapiro's score of acceptor site (range is from -13 [intron] to +1 [exon]) is: 100 * ((t1 - l1)/(h1 - l1) + (t2 - l2)/(h2 - l2))/2, where t1 is the sum of the best 8 of 10 percentages at positions -13 to -4, l1 is the sum of the lowest 8 of 10 percentages at position -13 to -4, h1 is the sum of the highest 8 of 10 percentages at positions -13 to -4, t2 is the sum of percentages at positions -3 to +1, l2 is the sum of the lowest percentages at positions -3 to +1, and h2 is the sum of the highest percentages at positions -3 to +1

1	shapiroAcceptor(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,site="acceptor")
acceptor.ss<-getSeq(bsgenome,splice_sites)
##sacceptor<-shapiroAcceptor(acceptor.m,acceptor.ss)