diff --git a/genesets/SupTab6_Krt13_Hillock.csv b/genesets/SupTab6_Krt13_Hillock.csv index 1fa9fc8244896fd65a42b5a8ee323db9f1670e93..d4ac03268d1128908dd915a783e2500a7a655fc5 100644 --- a/genesets/SupTab6_Krt13_Hillock.csv +++ b/genesets/SupTab6_Krt13_Hillock.csv @@ -1,9 +1,3 @@ -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 diff --git a/r.scripts/sc-TissueMapper_RUN.Pd.R b/r.scripts/sc-TissueMapper_RUN.Pd.R index 43ddd2502e0210315f4d6ba47d8c1da7e2746463..81cbf9a7a8ee33bf0dba5a209fdd5a4eefc06968 100644 --- a/r.scripts/sc-TissueMapper_RUN.Pd.R +++ b/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])