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?
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
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