geneSim: geneSim

In meshes: MeSH Enrichment and Semantic analyses

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

## hsamd <- meshdata("MeSH.Hsa.eg.db", category='A', computeIC=T, database="gendoo")
data(hsamd)
geneSim("241", "251", semData=hsamd, measure="Wang", combine="BMA")

Example output

Loading required package: DOSE

DOSE v3.2.0  For help: https://guangchuangyu.github.io/DOSE

If you use DOSE in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Guang-Rong Yan, Qing-Yu He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics 2015, 31(4):608-609


Attaching package: 'meshes'

The following object is masked from 'package:DOSE':

    geneSim

Warning message:
Couldn't set synchronous mode: database is locked
Use `synchronous` = NULL to turn off this warning. 
[1] 0.487

meshes documentation built on Nov. 8, 2020, 4:58 p.m.