RSEC run for vignette

Description

RSEC run for vignette

Format

ClusterExperiment object, the result of running RSEC on fluidigm data described in vignette and available in the scRNAseq package.

Author(s)

Elizabeth Purdom epurdom@stat.berkeley.edu

See Also

fluidigm

Examples

#code used to create rsecFluidigm:
## Not run: 
library(scRNAseq)
data("fluidigm")
se <- fluidigm[,colData(fluidigm)[,"Coverage_Type"]=="High"]
wh_zero <- which(rowSums(assay(se))==0)
pass_filter <- apply(assay(se), 1, function(x) length(x[x >= 10]) >= 10)
se <- se[pass_filter,]
fq <- round(limma::normalizeQuantiles(assay(se)))
assays(se) <- list(normalized_counts=fq)
wh<-which(colnames(colData(se)) %in% c("Cluster1","Cluster2"))
colnames(colData(se))[wh]<-c("Published1","Published2")
library(clusterExperiment)
ncores<-1
system.time(
  rsecFluidigm<-RSEC(se, 
                     isCount = TRUE, 
                     k0s = 4:15, 
                     alphas=c(0.1, 0.2, 0.3), 
                     betas = 0.9,
                     reduceMethod="PCA", 
                     nReducedDims=10,
                     minSizes=1, 
                     clusterFunction="hierarchical01",
                     consensusMinSize=3,
                     consensusProportion=0.7,
                     dendroReduce= "mad",
                     dendroNDims=1000,
                     mergeMethod="adjP",
	                    mergeDEMethod="limma",
                     mergeCutoff=0.01,
                     ncores=ncores, 
                     random.seed=176201)
)
metadata(rsecFluidigm)$packageVersion<-packageVersion("clusterExperiment")
## Tests that haven't changed the clustering results.
x<-unique(clusterMatrix(rsecFluidigm)[,"makeConsensus"])
y<-unique(clusterMatrix(rsecFluidigm)[,"mergeClusters"])
if(length(x[x>0]) != 8) 
  stop("rsecFluidigm object has changed -- makeConsensus")
if(length(y[y>0]) != 6) 
  stop("rsecFluidigm object has changed -- different # of mergeClusters")
adjPValues<-c(0.049794879, 0.007356062, 0.008204838, 
  0.013156033, 0.009336540, 0.007497524, 0.033526666)
if(nrow(rsecFluidigm@merge_nodeProp)!=length(adjPValues)) 
  stop("rsecFluidigm object has changed -- makeDendrogram")
if(!all.equal(adjPValues,rsecFluidigm@merge_nodeProp[,"adjP"])) 
  stop("rsecFluidigm object has changed -- different percentages")	
devtools::use_data(rsecFluidigm,overwrite=FALSE)

## End(Not run)