Fix hillock genelist csv and edit the Pd r.script to match

genesets/SupTab6_Krt13_Hillock.csv

-Supplementary Table 6,,,,
-Related to Extended Data 4g:  Krt4+/Krt13+ hillock-associated genes from 3' droplet-based scRNA-seq,,,,
-Thresholds: all genes shown,,,,
-,,,,
-,,,,
-,,,,
 Gene,log2 fold-change (means),log2 fold-change (MAST),p,FDR
 Ltf,4.371203488,1.997240249,2.12E-49,2.80E-47
 Krt4,2.883475949,2.715058937,3.95E-132,6.28E-129

r.scripts/sc-TissueMapper_RUN.Pd.R

@@ -339,7 +339,7 @@ sc10x <- SetIdent(object=sc10x,cells.use=names(sc10x@ident[sc10x@ident %in% c("S
 sc10x <- StashIdent(object=sc10x,save.name="mLin")
 
 gene.orthog <- read.delim("./genesets/Ensemble.mus-hum.txt")
-gene.set1 <- read_csv("./genesets/SupTab3_Consensus_Sigs.csv",skip=6)
+gene.set1 <- read_csv("./genesets/SupTab3_Consensus_Sigs.csv",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])
@@ -377,7 +377,7 @@ gene.set2 <- as.list(gene.set2)
 names(gene.set2) <- "Ionocyte"
 gene.set <- c(gene.set,gene.set2)
 rm(gene.set2)
-gene.set1 <- read_csv("./genesets/SupTab6_Krt13_Hillock.csv",skip=6)
+gene.set1 <- read_csv("./genesets/SupTab6_Krt13_Hillock.csv",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])