How to interpret DoubletDecon output?

[charlesgwellem]

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.