title: “AUC analysis for seurat object” output: html_notebook author: Dr Upasna Srivastava

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("AUCell")

library(AUCell)
library(Seurat)

load("SeuratData.Robj")
Sri <- UpdateSeuratObject(object = Sri)

Sri[[]]

DimPlot(object = Sri, group.by = "cell.types", label = TRUE)

markers <- read.csv("PanglaoDB_markers_27_Mar_2020.tsv", sep = "\t")
markers <- markers[markers$cell.type == "Endothelial cells" & markers$species != "Hs",]
markers

genes <- markers$official.gene.symbol

mousify <- function(a){
  return(paste0(substr(a,1,1), tolower(substr(a,2,nchar(a)))))
  
}
genes <- sapply(genes, mousify)
genes

counts <- GetAssayData(object = Sri, slot = "counts")

cell_rankings <- AUCell_buildRankings(counts)

cells_AUC <- AUCell_calcAUC(genes, cell_rankings)

cells_assignment <- AUCell_exploreThresholds(cells_AUC, plotHist = TRUE, assign=TRUE)

cells_assignment$geneSet$assignment

new_cells <- names(which(getAUC(cells_AUC)["geneSet",]>0.15))

Sri$Diagonosis <- ifelse(colnames(tiss) %in% new_cells, "Disease", "Normal")

Sri[[]]

DimPlot(object = Sri, group.by = "Diagonosis", label = TRUE)

DimPlot(object = Sri, group.by = "cell.types", label = TRUE)