[BioC] problem with the CoCiteStats and mouseLLMappings libraries

[mattia]

Dear all, 

I have a problem with the CoCiteStats library.
I have attached what I have done for determining the co-citation pValue 
between two human LLids. In this case all is working fine:

> library(CoCiteStats)
Loading required package: humanLLMappings
> hLLids<-ls(humanLLMappingsLL2PMID)
> hnumPapers <- length(unique(unlist(as.list(humanLLMappingsLL2PMID))))
> hPaperLen <- paperLen(ls(humanLLMappingsLL2PMID))$Counts
> length(hPaperLen)
[1] 111318
> hPaperLen[1:5]
 2591067  3458201  3610142  8889549 12477932
       1        1        1       81    15868
> gene.geneslist.sig(gene=hLLids[1], geneslist=hLLids[2], 
numPapers=hnumPapers, PaperLen=hPaperLen, n.resamp=50)
$statistic
          Concordance      Jaccard        Hubert
original 1.000000e+00 1.388889e-02  0.0436623687
gs       9.403273e-01 8.873752e-01  0.8806545584
ps       6.301991e-05 1.148339e-06 -0.0001406189
both     1.520238e-01 8.226504e-02 -0.6959523497

$pval
         Concordance Jaccard Hubert
original        0.24    0.72   0.72
gs              0.72    0.72   0.72
ps              0.32    0.72   1.00
both            0.72    0.72   0.72


Rather, if I try to repeat the same code for two mouse LLids:

>
> library(mouseLLMappings)
> mLLids<-ls(mouseLLMappingsLL2PMID)
> mnumPapers<-length(unique(unlist(as.list(mouseLLMappingsLL2PMID))))
> mPaperLen <- paperLen(ls(mouseLLMappingsLL2PMID))$Counts
> length(mPaperLen)
[1] 0
> mPaperLen
numeric(0)

..therefore it seems to me that there is some problem either in the paperLen 
function or in the mouseLLMappings library. The latter is properly installed 
and working in my opinion.
I tried to obtain the same result of the paperLen function using the following 
line of code, to test if I am able to overcame the problem and use the 
gene.geneslist.sig function, but I get an error message :

> mPaperLen<-table(unlist(as.list(mouseLLMappingsLL2PMID)))
> length(mPaperLen)
[1] 40683
> mPaperLen[1:5]
     100 10021335 10021340 10021343 10021344
       1        1        1        1        1
> gene.geneslist.sig(gene=mLLids[1], geneslist=mLLids[2], 
numPapers=mnumPapers, PaperLen=mPaperLen, n.resamp=50)
Error in wh$papers[[g1]] : subscript out of bounds


I also unsuccessfully tried by using the old mouseLLMappings 1.8 and the 
developmental CoCiteStats_1.3.0 versions..

Thanks for any suggestion

> sessionInfo()
R version 2.2.1, 2005-12-20, x86_64-unknown-linux-gnu

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

other attached packages:
mouseLLMappings     CoCiteStats humanLLMappings
       "1.10.0"         "1.2.0"        "1.10.0"
>
-- 
Mattia Pelizzola
PhD Student
Genopolis Consortium
Milano-Bicocca University
P.zza della Scienza 4
20126 Milano (Italy)
tel:+390264483556
fax:+390264483552