Question: problem with the CoCiteStats and mouseLLMappings libraries
0
13.5 years ago by
mattia80
mattia80 wrote:
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
cocitestats • 357 views