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

1
gene.geneslist.sig(gene, geneslist, paperLens = paperLen(), n.resamp=100)

Arguments

gene

The Entrez Gene ID for the gene of interest.

geneslist

The list of Entrez Gene IDs for genes with which the co-citation of the gene of interest is to be evaluated.

paperLens

The sizes of the PubMed papers for consideration.

n.resamp

Number of resampling for generating empirical p-values.

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

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gene <- "705"
geneslist <- "7216"

gene.geneslist.sig(gene, geneslist, n.resamp=50)