Add QuSAGE to mouse lineage from scRNA-Seq (Montoro et al)

r.scripts/sc-TissueMapper_RUN.Pd.R

@@ -3,6 +3,7 @@ library(methods)
 library(optparse)
 library(Seurat)
 library(readr)
+library(readxl)
 library(fBasics)
 library(pastecs)
 library(qusage)
@@ -260,7 +261,59 @@ names(gene.set1) <- "CGC"
 gene.set<- c(gene.set,gene.set1)
 rm(gene.set1)
 gc()
-results.cor.Epi.lgea <- scQuSAGEsm(sc10x.Epi,gs=gene.set,ds=opt$ds,nm="Epi.dws.sc",folder="lgea")
+results.cor.Epi.lgea <- scQuSAGEsm(sc10x.Epi,gs=gene.set,ds=opt$ds,nm="Epi.dws.sub",folder="lgea")
+rm(gene.set)
+
+gene.orthog <- read.delim("./genesets/Ensemble.mus-hum.txt")
+gene.set1 <- read_excel("./genesets/SupTab3_Consensus_Sigs.xlsx",skip=5)
+gene.set2 <- as.data.frame(gene.set1$Basal[!is.na(gene.set1$Basal)])
+colnames(gene.set2) <- "genes"
+gene.set2 <- as.data.frame(merge(gene.set2,gene.orthog,by.x="genes",by.y="Gene.name")[,4])
+gene.set2 <- as.list(gene.set2)
+names(gene.set2) <- "Basal"
+gene.set <- c(gene.set2)
+gene.set2 <- as.data.frame(gene.set1$Club[!is.na(gene.set1$Club)])
+colnames(gene.set2) <- "genes"
+gene.set2 <- as.data.frame(merge(gene.set2,gene.orthog,by.x="genes",by.y="Gene.name")[,4])
+gene.set2 <- as.list(gene.set2)
+names(gene.set2) <- "Club"
+gene.set <- c(gene.set,gene.set2)
+gene.set2 <- as.data.frame(gene.set1$Ciliated[!is.na(gene.set1$Ciliated)])
+colnames(gene.set2) <- "genes"
+gene.set2 <- as.data.frame(merge(gene.set2,gene.orthog,by.x="genes",by.y="Gene.name")[,4])
+gene.set2 <- as.list(gene.set2)
+names(gene.set2) <- "Ciliated"
+gene.set <- c(gene.set,gene.set2)
+gene.set2 <- as.data.frame(gene.set1$Tuft[!is.na(gene.set1$Tuft)])
+colnames(gene.set2) <- "genes"
+gene.set2 <- as.data.frame(merge(gene.set2,gene.orthog,by.x="genes",by.y="Gene.name")[,4])
+gene.set2 <- as.list(gene.set2)
+names(gene.set2) <- "Tuft"
+gene.set <- c(gene.set,gene.set2)
+gene.set2 <- as.data.frame(gene.set1$Neuroendocrine[!is.na(gene.set1$Neuroendocrine)])
+colnames(gene.set2) <- "genes"
+gene.set2 <- as.data.frame(merge(gene.set2,gene.orthog,by.x="genes",by.y="Gene.name")[,4])
+gene.set2 <- as.list(gene.set2)
+names(gene.set2) <- "Neuroendocrine"
+gene.set <- c(gene.set,gene.set2)
+gene.set2 <- as.data.frame(gene.set1$Ionocyte[!is.na(gene.set1$Ionocyte)])
+colnames(gene.set2) <- "genes"
+gene.set2 <- as.data.frame(merge(gene.set2,gene.orthog,by.x="genes",by.y="Gene.name")[,4])
+gene.set2 <- as.list(gene.set2)
+names(gene.set2) <- "Ionocyte"
+gene.set <- c(gene.set,gene.set2)
+rm(gene.set2)
+gene.set1 <- read_excel("./genesets/SupTab6_Krt13_Hillock.xlsx",skip=5)
+gene.set1 <- gene.set1[gene.set1$FDR<=0.05 & gene.set1$'log2 fold-change (MAST)'>=1.5,1]
+colnames(gene.set1) <- "genes"
+gene.set1 <- as.data.frame(merge(gene.set1,gene.orthog,by.x="genes",by.y="Gene.name")[,4])
+gene.set1 <- as.list(gene.set1)
+names(gene.set1) <- "Hillock"
+gene.set <- c(gene.set,gene.set1)
+rm(gene.set1)
+rm(gene.orthog)
+gene.set <- lapply(gene.set,droplevels)
+results.cor.Epi.MusLungHierarchy <- scQuSAGEsm(sc10x.Epi,gs=gene.set,ds=opt$ds,nm="Epi.dws.sub",folder="MusLungHierarchy")
 rm(gene.set)
 
 sc10x.St <- scCluster(sc10x.St,pc.use=opt$acca,res.use=opt$res.st,folder="st",red="cca.aligned")