[BioC] The funcion getOrfs, doesn`t works, package: GeneR

[avargas]

I apreciate the quick response, here is my code:

> library("GeneR")
> s<-"gtcatgcatgctaggtgacagttaaaatgcgtctaggtgacagtctaacaa"
> placeString(s)
[1] 0
> 
> getOrfs(phase = NULL,seqno=0)
NULL
> maxOrf()
[1] -1
> 
> #Problem with exact word

> placeString("TTTTTTTTTTTT")
[1] 0
> exactWord("TTT")
[[1]]
[1] -1

> sessionInfo()
R version 2.10.0 Under development (unstable) (2009-08-15 r49252) 
i386-pc-mingw32 

locale:
[1] LC_COLLATE=Spanish_Mexico.1252  LC_CTYPE=Spanish_Mexico.1252   
[3] LC_MONETARY=Spanish_Mexico.1252 LC_NUMERIC=C                   
[5] LC_TIME=Spanish_Mexico.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] GeneR_2.15.0

On Fri, 9 Oct 2009 04:21:58 -0400, Vincent Carey
<stvjc at channing.harvard.edu> wrote:
> Please give sessionInfo() result.  Here are my results, installing
> GeneR from source a moment ago
> 
>> s<-"gtcatgcatgctaggtgacagttaaaatgcgtctaggtgacagtctaacaa"
>> placeString(s)
> [1] 0
>> s
> [1] "gtcatgcatgctaggtgacagttaaaatgcgtctaggtgacagtctaacaa"
>> ?placeString
>>    getSeq(seqno=0)
> [1] "GTCATGCATGCTAGGTGACAGTTAAAATGCGTCTAGGTGACAGTCTAACAA"
>> getOrfs(phase = NULL,seqno=0)
>      start stop
> [1,]     4   18
> [2,]     8   25
>> maxOrf()
> [1] 18
>> ?maxOrf
>> ?getOrfs
>> getOrfs(phase = NULL,seqno=0)
>      start stop
> [1,]     4   18
> [2,]     8   25
>> placeString("TTTTTTTTTTTT")
> [1] 0
>> exactWord("TTT")
> [[1]]
>  [1]  1  2  3  4  5  6  7  8  9 10
> 
>> sessionInfo()
> R version 2.10.0 Under development (unstable) (2009-09-09 r49642)
> i386-apple-darwin9.8.0
> 
> locale:
> [1] C
> 
> attached base packages:
> [1] stats     graphics  grDevices datasets  tools     utils     methods
> [8] base
> 
> other attached packages:
> [1] GeneR_2.15.0    weaver_1.11.1   codetools_0.2-2 digest_0.3.1
> 
> 
> 
> On Fri, Oct 9, 2009 at 1:04 AM, avargas <avargas at lcg.unam.mx> wrote:
>> Dear list, i have some troubles with the GeneR package, it seems that
>> getOrfs is not working. I already try to use it with the example info of
>> the help:
>>
>> library("GeneR")
>> s<-"gtcatgcatgctaggtgacagttaaaatgcgtctaggtgacagtctaacaa"
>> placeString(s)
>>
>> getOrfs(phase = NULL,seqno=0)
>> maxOrf()
>>
>> But returns:
>>> getOrfs(phase = NULL,seqno=0)
>> NULL
>>> maxOrf()
>> [1] -1
>> I have the version 2.10 of R and the Package GeneR version 2.15.0
>> I mean, the examples of
>> http://rss.acs.unt.edu/Rdoc/library/GeneR/doc/GeneR.pdf at page 5 are
> not
>> reproducible, so, which is the problem?
>> In advance, thanks.
>>
>> Amhed Missael Vargas Velàzquez
>> avargas at lcg.unam.mx
>> LCG,UNAM
>>
>> Pd: I think that the problem is with another function named, exact word,
>> that does not work too.
>> i.e.
>> library("GeneR")
>> placeString("TTTTTTTTTTTT")
>> exactWord("TTT")
>>
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