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.
vector of strings or DNAStringSet of reference splice list
vector of strings or DNAStringSet of fasta to score
data.frame with Shapiro scores
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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)
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