simData: Simulated data for running examples

Description Format Details Author(s) Examples

Description

Simulated data for running examples

Format

Three objects are loaded, two data frame(s) of simulated data each with 300 samples/columns and 153 variables/rows, and a vector of length 300 with the true cluster assignments.

Details

simData is simulated normal data of 300 observations with 51 relevant variables and the rest of the variables being noise, with observations being in one of 3 groups. simCount is simulated count data of the same dimensions. trueCluster gives the true cluster identifications of the samples. The true clusters are each of size 100 and are in order in the columns of the data.frames.

Author(s)

Elizabeth Purdom [email protected]

Examples

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#code used to create data:
nvar<-51 #multiple of 3
n<-100
x<-cbind(matrix(rnorm(n*nvar,mean=5),nrow=nvar),
 matrix(rnorm(n*nvar,mean=-5),nrow=nvar),
          matrix(rnorm(n*nvar,mean=0),nrow=nvar))
#make some of them flipped effects (better for testing if both sig under/over
#expressed variables)
geneGroup<-sample(rep(1:3,each=floor(nvar/3)))
gpIndex<-list(1:n,(n+1):(n*2),(2*n+1):(n*3))
x[geneGroup==1,]<-x[geneGroup==1,unlist(gpIndex[c(3,1,2)])]
x[geneGroup==2,]<-x[geneGroup==2,unlist(gpIndex[c(2,3,1)])]

#add in differences in variable means
smp<-sample(1:nrow(x),10)
x[smp,]<-x[smp,]+10

#make different signal y
y<-cbind(matrix(rnorm(n*nvar,mean=1),nrow=nvar),
         matrix(rnorm(n*nvar,mean=-1),nrow=nvar),
         matrix(rnorm(n*nvar,mean=0),nrow=nvar))
y<-y[,sample(1:ncol(y))]+ matrix(rnorm(3*n*nvar,sd=3),nrow=nvar)

#add together the two signals
simData<-x+y

#add pure noise variables
simData<-rbind(simData,matrix(rnorm(3*n*nvar,mean=10),nrow=nvar),
               matrix(rnorm(3*n*nvar,mean=5),nrow=nvar))
#make count data
countMean<-exp(simData/2)
simCount<-matrix(rpois(n=length(as.vector(countMean)), lambda
=as.vector(countMean)+.1),nrow=nrow(countMean),ncol=ncol(countMean))
#labels for the truth
trueCluster<-rep(c(1:3),each=n)
#save(list=c("simCount","simData","trueCluster"),file="data/simData.rda")

Bioconductor-mirror/clusterExperiment documentation built on Aug. 2, 2017, 4:28 p.m.