clusterSim: clusterSim

View source: R/clusterSim.R

clusterSimR Documentation

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 Aug. 27, 2024, 10:59 a.m.