mclusterSim: mclusterSim

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

mclusterSim

Description

Pairwise semantic similarity for a list of gene clusters

Usage

mclusterSim(
  clusters,
  ont = "DO",
  organism = "hsa",
  measure = "Wang",
  combine = "BMA"
)

Arguments

clusters	A list of gene clusters
ont	one of "DO" and "MPO"
organism	organism
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.

Value

similarity matrix

Author(s)

Yu Guangchuang

Examples

cluster1 <- c("835", "5261","241")
cluster2 <- c("578","582")
cluster3 <- c("307", "308", "317")
clusters <- list(a=cluster1, b=cluster2, c=cluster3)
mclusterSim(clusters, measure="Wang")

YuLab-SMU/DOSE documentation built on April 15, 2024, 9:27 p.m.