twowayTable: Compute a two way co-citation table for 2 genes.

Description

This function computes a two way table for comparing co-citation, in PubMed for the two input genes. The values in the table can be adjusted according to either the paper size or the gene size.

Usage

twowayTable(g1, g2, weights = TRUE, paperLens=paperLen())

Arguments

The EntrezGene identifier for gene 1.

The EntrezGene identifier for gene 2.

weights

TRUE or FALSE indicating whether paper size weights should be used.

paperLens

A vector containing the number of genes each paper refers to, or cites.

Value

A vector of length four, with entries n11, n12, n21 and n22. These correspond to the number of papers that cite both genes, the number that cite only gene 1, the number that cite only gene 2, and the total number of papers minus those counted in n11, n21, n12, or in the default case the weighted versions of these quantities.

Details

To determine the association between two genes one can use co-citation in the medical literature. When weights is FALSE this function computes the number of papers that cite only gene 1, only gene 2, both and neither.

By default, we use the org.Hs.eg.db package to define the set of papers that are used in the computations. For other organisms, or for more restricted sets of papers the user will need to supply the vector paperLens explicitly.

One can consider papers which cite many genes to be less informative than those that cite only a few genes. If weights is TRUE (the default) then papers are weighted by the inverse of the number of citations.

Examples

Run this code


  pL = paperLen()
  twowayTable("10", "100", paperLens=pL)
  twowayTable("10", "100", FALSE, paperLens=pL)