R help - Nov 2011 - Problem with substr

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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Hi,

On Tue, Nov 15, 2011 at 4:31 PM, sophy1987 <yatingcheng.marina at
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