shapiroDonor: shapiroDonor

In dianalow/SPLINTER: Splice Interpreter of Transcripts

shapiroDonor

Description

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.

Usage

shapiroDonor(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

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)
donor.ss<-getSeq(bsgenome,splice_sites)
##sdonor<-shapiroDonor(donor.m,donor.ss)

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