gene.geneslist.sig: Compute 3 two-way table statistics and p-values, with 4...

In Bioconductor/CoCiteStats: Different test statistics based on co-citation.

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 \Gamma 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, 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

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

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

Bioconductor/CoCiteStats documentation built on Nov. 2, 2024, 6:34 a.m.