shapiroAcceptor {SPLINTER} | R Documentation |
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
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)