geneSim: geneSim

In GuangchuangYu/meshes: MeSH Enrichment and Semantic analyses

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 Oct. 31, 2024, 10:12 a.m.