clusterSim: clusterSim

In YuLab-SMU/DOSE: Disease Ontology Semantic and Enrichment analysis

clusterSim

Description

semantic similarity between two gene clusters

Usage

clusterSim(
  cluster1,
  cluster2,
  ont = "HDO",
  organism = "hsa",
  measure = "Wang",
  combine = "BMA"
)

Arguments

cluster1	a vector of gene IDs
cluster2	another vector of gene IDs
ont	one of "HDO", "HPO" and "MPO"
organism	one of "hsa" and "mmu"
measure	One of "Resnik", "Lin", "Rel", "Jiang" and "Wang" methods.
combine	One of "max", "avg", "rcmax", "BMA" methods, for combining

Details

given two gene clusters, this function calculates semantic similarity between them.

Value

similarity

Author(s)

Yu Guangchuang

Examples

## Not run: 
cluster1 <- c("835", "5261","241", "994")
cluster2 <- c("307", "308", "317", "321", "506", "540", "378", "388", "396")
clusterSim(cluster1, cluster2)

## End(Not run)

YuLab-SMU/DOSE documentation built on Nov. 3, 2024, 9:37 p.m.