ClusterPurity: A function to measure cluster purity

In IntNMF: Integrative Clustering of Multiple Genomic Dataset

Description

Given the true clustering assignment for the subjects, this function calculates cluster purity index comparing with clustering assignment determined by integrative NMF algorithm. Higher value of cluster purity indicates better cluster predictive discrimination.

Usage

ClusterPurity(ComputedClusters, TrueClasses)

Arguments

ComputedClusters	Clustering assignment determined by integrative NMF algorithm
TrueClasses	True clustering assignment of the subjects

Value

Cluster purity index value

Author(s)

Prabhakar Chalise, Rama Raghavan, Brooke Fridley

References

Kim Hyunsoo and Park Haesun (2007). Sparse non-negative matrix factorization via alternating non-negativity constrained least squares for microarray data analysis. Bioinformatics, 23: 1495-1502.

Examples

prop <- c(0.20,0.30,0.27,0.23)
effect <- 2.5
sim.D <- InterSIM(n.sample=100,cluster.sample.prop=prop,delta.methyl=effect,
delta.expr=effect,delta.protein=effect,p.DMP=0.25,p.DEG=NULL,p.DEP=NULL,
do.plot=FALSE, sample.cluster=TRUE, feature.cluster=TRUE)

dat1 <- sim.D$dat.methyl
dat2 <- sim.D$dat.expr
dat3 <- sim.D$dat.protein
true.cluster.assignment <- sim.D$clustering.assignment

## Make all data positive by shifting to positive direction.
## Also rescale the datasets so that they are comparable.
if (!all(dat1>=0)) dat1 <- pmax(dat1 + abs(min(dat1)), .Machine$double.eps)
dat1 <- dat1/max(dat1)
if (!all(dat2>=0)) dat2 <- pmax(dat2 + abs(min(dat2)), .Machine$double.eps)
dat2 <- dat2/max(dat2)
if (!all(dat3>=0)) dat3 <- pmax(dat3 + abs(min(dat3)), .Machine$double.eps)
dat3 <- dat3/max(dat3)

# The function nmf.mnnals requires the samples to be on rows and variables on columns.
dat <- list(dat1,dat2,dat3)
fit <- nmf.mnnals(dat=dat,k=length(prop),maxiter=200,st.count=20,n.ini=15,ini.nndsvd=TRUE,
seed=TRUE)
ClusterPurity(ComputedClusters=fit$clusters, TrueClasses=true.cluster.assignment$cluster.id)

Example output

Loading required package: MASS
Loading required package: NMF
Loading required package: pkgmaker
Loading required package: registry
Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [OK] | Cores 2/2
Loading required package: mclust
Package 'mclust' version 5.4.3
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: InterSIM
Loading required package: tools
There were 18 warnings (use warnings() to see them)
[1] 1

IntNMF documentation built on May 1, 2019, 6:35 p.m.