Hi, On Tue, Nov 15, 2011 at 4:31 PM, sophy1987 <yatingcheng.mar...@gmail.com> wrote: > Hi, everyone > When I ran this cript, There is Error in substring(tmp.subject, tmp.end[ex] > + 1, tmp.start[ex + 1] - 1) : > invalid substring argument(s) > > Could someone figure out what the problem is?
Not without a reproducible example. We don't know what tmp.subject is, or tmp.start or tmp.end, since they're both derived from tmp.align and we don't have that either. Presumably there's something wrong with one of the arguments to substring, but there's no way we can figure out which one. Sarah > for(i in 1:length(genebody[,1])){ > > tmp.id<-as.vector(genebody[i,1]) > # get gene id > tmp.subject<-as.vector(genebody[i,2]) > # get gene sequence > tmp.exons<-exons[which(exons[,1]==tmp.id),] > # get exons of the > selected genes > > tmp.pattern<-as.vector(tmp.exons[,3]) > # define exons as patterns > for alignment > tmp.align<-pairwiseAlignment(pattern=tmp.pattern, > subject=tmp.subject,type="local") # align all exons > pairwise to gene > sequence > tmp.start<-start(subject(tmp.align)) > # vector of all alignment > starts > tmp.end<-end(subject(tmp.align)) > # vector of all alignment > ends > > for(ex in 1:(length(tmp.end)-1)){ > # extract introns > > tmp.intron<-substr(tmp.subject,tmp.end[ex]+1,tmp.start[ex+1]-1) > > > introns<-rbind(introns,cbind(tmp.id,tmp.end[ex]+1,tmp.start[ex+1]-1,tmp.intron)) > > } > > } > > > Thank you -- Sarah Goslee http://www.functionaldiversity.org ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.