shapiroAcceptor: shapiroAcceptor

In dianalow/SPLINTER: Splice Interpreter of Transcripts

shapiroAcceptor

Description

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

Usage

shapiroAcceptor(reference_fasta, target_fasta)

Arguments

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

Value

data.frame with Shapiro scores

Author(s)

Diana Low

See Also

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

Examples

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)

dianalow/SPLINTER documentation built on March 28, 2024, 2:07 p.m.