rsecFluidigm {clusterExperiment} | R Documentation |
RSEC run for vignette
ClusterExperiment object, the result of running RSEC
on
fluidigm data described in vignette and available in the scRNAseq
package.
Elizabeth Purdom epurdom@stat.berkeley.edu
#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)