Open charlesgwellem opened 4 years ago
Hi. Thank you for this great package. Which information from the results of running DoubletDecon output gives me information about which cell in my Seurat data set is a doublet? I have used the following code from the standard tutorial.
location="/Users/xxx/xxx/" #Update as needed <s> #Seurat_Pre_Process() expressionFile=paste0(location, "counts.txt") genesFile=paste0(location, "Top50Genes.txt") clustersFile=paste0(location, "Cluster.txt") newFiles=Seurat_Pre_Process(expressionFile, genesFile, clustersFile) </s> #Improved_Seurat_Pre_Process() seuratObject=readRDS("seurat.rds") newFiles=Improved_Seurat_Pre_Process(seuratObject, num_genes=50, write_files=FALSE) filename="PBMC_example" write.table(newFiles$newExpressionFile, paste0(location, filename, "_expression"), sep="\t") write.table(newFiles$newFullExpressionFile, paste0(location, filename, "_fullExpression"), sep="\t") write.table(newFiles$newGroupsFile, paste0(location, filename , "_groups"), sep="\t", col.names = F) results=Main_Doublet_Decon(rawDataFile=newFiles$newExpressionFile, groupsFile=newFiles$newGroupsFile, filename=filename, location=location, fullDataFile=NULL, removeCC=FALSE, species="hsa", rhop=1.1, write=TRUE, PMF=TRUE, useFull=FALSE, heatmap=FALSE, centroids=TRUE, num_doubs=100, only50=FALSE, min_uniq=4, nCores=-1)
Thank you in advance for your kind help.
Hi. Thank you for this great package. Which information from the results of running DoubletDecon output gives me information about which cell in my Seurat data set is a doublet? I have used the following code from the standard tutorial.
Thank you in advance for your kind help.