geneSim: geneSim

View source: R/geneSim.R

geneSimR Documentation

geneSim

Description

semantic similarity between two gene vector

Usage

geneSim(geneID1, geneID2 = NULL, measure = "Wang", combine = "BMA", semData)

Arguments

geneID1

gene ID vector

geneID2

gene ID vector

measure

one of "Wang", "Resnik", "Rel", "Jiang" and "Lin"

combine

One of "max", "avg", "rcmax", "BMA" methods, for combining semantic similarity scores of multiple DO terms associated with gene/protein.

semData

gene annotation data for semantic measurement

Value

score matrix

Author(s)

Guangchuang Yu

Examples

## library(meshes)
## library(AnnotationHub)
## ah <- AnnotationHub()
## qr_hsa <- query(ah, c("MeSHDb", "Homo sapiens"))
## filepath_hsa <- qr_hsa[[1]]
## db <- MeSHDbi::MeSHDb(filepath_hsa)
## hsamd <- meshdata(db, category='A', computeIC=T, database="gendoo")
data(hsamd)
geneSim("241", "251", semData=hsamd, measure="Wang", combine="BMA")

GuangchuangYu/meshes documentation built on Nov. 12, 2022, 7:13 a.m.