epurdom
giving paramMatrix gives error.
From vignette, gives error:
se<-fluidigm[,colData(fluidigm)[,"Coverage_Type"]=="High"] whLow<-which(rowSums(assay(se))<100) se<-se[-whLow,]
checkParam<-clusterMany(se, clusterFunction="pam",ks=2:10,findBestK=TRUE,removeSil=c(TRUE), isCount=TRUE,dimReduce=c("PCA","mostVar"),nVarDims=c(100,500,1000),nPCADims=c(5,15,50),run=FALSE) ce<-clusterMany(se, paramMatrix=checkParam$paramMatrix, clusterDArgs=checkParam$clusterDArgs, seqArgs=checkParam$seqArgs,subsampleArgs=checkParam$subsampleArgs)
Problem is that dimensionality reduction is done BEFORE giving param Matrix to the most basic version. Need to read paramMatrix and figure out dimReduce parameters... And, column of paramMatrix does NOT include that information (because done before hand, so in list). This is actually really tricky...
This also has some urgency because vignette talks about doing this, but it doesn't work. Might need to delete out of vignette for now and some back to this.