calSim: Function to calculate similarity score

In FSim: A package to search functionally similar genes

Description

The function can be used to calculate similarity scores between two genes or gene and GO terms.

Usage

calSim(g1, g2 = NULL, tids = NULL, ontology = "ALL", an.go = NULL,
term2ancestor = TRUE, count = FALSE)

Arguments

g1	The first gene ID to compare.
g2	The second gene ID to compare.
tids	The GO term IDs to compare if the second gene ID is NULL.
ontology	The GO ontology. It can be "BP", "MF", "CC" and "ALL".
an.go	The R enviroment that provide mappings between gene IDs and GO IDs including their ancestors.
term2ancestor	The option works when terms is not NULL. If TRUE, the input term and their ancestor terms will be used. If FALSE, the input term will be used directly.
count	Some ancestor GO terms can be counted serveral times for the same gene. If count is TRUE, the count number will be a weight in the calculation. If count is FALSE, the counts will not be used.

Value

The returned values include Kappa value, Approximate Standard Error (ASE) and Z value.

Author(s)

Qiang Hu

See Also

SearchGene

Examples

g1 <- "9"
g2 <- "10"
calSim(g1, g2, an.go=an.Hs.egGO, ontology="ALL", count=FALSE)

FSim documentation built on May 2, 2019, 6:30 p.m.