Shamit, The bug has been fixed and you could also directly input a DNAStringSet object as inputFilePath. Please let me know if you encounter any problem. Many thanks for catching and reporting this bug! Best regards, Julie On 7/10/14 10:56 AM, "Shamit Soneji" <shamit.soneji at="" med.lu.se=""> wrote: > Hi Julie, > > My name is Shamit, I'm a bioinformatican at Lund University Sweden who > has been asked by a colleague to find CRISPR sites for promoters in the > human genome. I was looking at your package, specifically the findgRNAs > function. > > I modified it slightly so that it would take a preloaded DNAStringSet > rather than having to load it from a file, but I've noticed the number > of found gRNAs is always from the last sequence in the input fasta. > > In short the function you have is: > > findgRNAs <- function(inputFilePath, .......){ > > subjects <- readDNAStringSet(inputFilePath, format > > > for(i in 1:length(subjects){ > #does stuff here > } > > > all.gRNAs # the returned object > > } > > > Maybe I'm not understanding how this works, but "all.gRNAs" is not > initialised outside the scope of the for-loop, and it is not appended to > in the loop so it never "grows". > > If I run the function with the first 3 sequences, ie: > > crtest <- findgRNAs(promoters[1:3],.....) > > length(crtest) >> 60 > > > Now... > > if I run each one individually: > > crtest <- findgRNAs(promoters[1],.....) > > length(crtest) >> 61 > > crtest <- findgRNAs(promoters[2],.....) > > length(crtest) >> 56 > > crtest <- findgRNAs(promoters[3],.....) > > length(crtest) >> 60 #which is the same as the first run trying 3 sequences at once. > > > Am I right in saying that I should get 61+56+60=177 gRNAs when I run the > function for promoters[1:3]? I just find the fact all.gRNAs doesn't grow > in the loop. > > If you could please tell me whether this is a bug, or whether I'm being > stupid I would appreciate it! > > Best, > > Shamit > > > > > > > > > > > > > >