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,reduceMethod="PCA",nReducedDims=10, ncores=ncores,random.seed=176201, clusterFunction="hierarchical01", combineMinSize=3)) packageVersion("clusterExperiment") devtools::use_data(rsecFluidigm,overwrite=FALSE) ## End(Not run)