[BioC] CRISPRseek: findgRNAs bug?

Zhu, Lihua (Julie) Julie.Zhu at umassmed.edu
Thu Jul 10 23:18:39 CEST 2014


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
> 
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> 



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