gene.geneslist.sig {CoCiteStats}R Documentation

Compute 3 two-way table statistics and p-values, with 4 different adjustments, for PubMed co-citation

Description

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

Usage

gene.geneslist.sig(gene, geneslist, numPapers, PaperLen, n.resamp=100)

Arguments

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.

Details

Value

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.

Author(s)

Beiying Ding

References

Testing Gene Associations Using Co-citation, by B. Ding and R. Gentleman. Bioconductor Technical Report, 2004

See Also

actorAdjTable,paperLen, twTStats, twowayTable

Examples

 
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)
  


[Package CoCiteStats version 1.2.0 Index]