Update load to handel cellranger v3 and different species/references

r.scripts/sc-TissueMapper_RUN.R

@@ -25,7 +25,7 @@ project.name="PdPbPc"
 
 scFolders()
 
-sc10x <- scLoad(p=project.name)
+sc10x <- scLoad(p=project.name,cellranger=2,ref="GRCh38")
 
 lg=500
 hg=3000

r.scripts/sc-TissueMapper_functions.R

@@ -23,7 +23,7 @@ scFolders <- function(){
 }
 
 
-scLoad <- function(p,mc=3,mg=200,sub=FALSE){
+scLoad <- function(p,mc=3,mg=200,sub=FALSE,cellranger=3,ref="GRCh38"){
   #Load and prefilter filtered_gene_bc_matrices_mex output from cellranger
   
   #Inputs:
@@ -37,9 +37,17 @@ scLoad <- function(p,mc=3,mg=200,sub=FALSE){
   
   #Load filtered_gene_bc_matrices_mex output from cellranger
   if (sub==FALSE){
-    sc10x.data <- Read10X(data.dir="./analysis/DATA/10x/filtered_gene_bc_matrices_mex/GRCh38/")
+    if (cellranger==2){
+      sc10x.data <- Read10X(data.dir=paste0("./analysis/DATA/10x/filtered_gene_bc_matrices_mex/",ref,"/"))
+    } else {
+      sc10x.data <- Read10X(data.dir=paste0("./analysis/DATA/10x/filtered_feature_bc_matrix/"))
+    }
   } else {
-    sc10x.data <- Read10X(data.dir=paste0("./analysis/DATA/",p,"/10x/filtered_gene_bc_matrices_mex/GRCh38/"))
+    if (cellranger==2){
+      sc10x.data <- Read10X(data.dir=paste0("./analysis/DATA/",p,"/10x/filtered_gene_bc_matrices_mex/GRCh38/"))
+    } else {
+      sc10x.data <- Read10X(data.dir=paste0("./analysis/DATA/",p,"/10x/filtered_feature_bc_matrix/"))
+    }
   }
   sc10x <- new("seurat",raw.data=sc10x.data)