gene.geneslist.sig {CoCiteStats} | R Documentation |
This function calculates Concordance, Jaccard's index and Hubert's $Γ$ with no adjustment, adjusting for paper size (PS), adjusting for gene size (GS) and both, to evaluate the significance of co-citation of a gene of interest and a gene list
gene.geneslist.sig(gene, geneslist, numPapers, PaperLen, n.resamp=100)
gene |
Gene of interest. |
geneslist |
The gene list with which the co-citation of the gene of interest is to be evaluated. |
numPapers |
Total number of PubMed papers for consideration. Default is all PubMed papers in the humanLLMappings package. |
PaperLen |
The sizes of the PubMed papers for consideration. Default is the paper size of all the PubMed papers in the humanLLMappings package. |
n.resamp |
Number of resampling for generating empirical p-values. |
Statistics and resampling p-values for all 3 two-way tables along with the
4 adjustments for gene
and geneslist
based on
n.resamp
resamplings.
Beiying Ding
Testing Gene Associations Using Co-citation, by B. Ding and R. Gentleman. Bioconductor Technical Report, 2004
actorAdjTable
,paperLen
,
twTStats
, twowayTable
gene <- "705" geneslist <- "7216" numPapers <- length(unique(unlist(eapply(humanLLMappingsLL2PMID, function(x) x)))) PaperLen <- paperLen(ls(humanLLMappingsLL2PMID))$Counts gene.geneslist.sig(gene, geneslist, numPapers, PaperLen, n.resamp=50)