Commit 730114a6 authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Fix aggregation.csv file load for cellranger 3

parent e11be2da
...@@ -53,9 +53,17 @@ scLoad <- function(p,mc=3,mg=200,sub=FALSE,cellranger=3,ref="GRCh38"){ ...@@ -53,9 +53,17 @@ scLoad <- function(p,mc=3,mg=200,sub=FALSE,cellranger=3,ref="GRCh38"){
#Label sample names from aggregation_csv.csv #Label sample names from aggregation_csv.csv
if (sub==FALSE){ if (sub==FALSE){
sc10x.aggr <- read_csv("./analysis/DATA/10x/aggregation_csv.csv") if (cellranger==2){
sc10x.aggr <- read_csv("./analysis/DATA/10x/aggregation_csv.csv")
} else {
sc10x.aggr <- read_csv("./analysis/DATA/10x/aggregation.csv")
}
} else { } else {
sc10x.aggr <- read_csv(paste0("./analysis/DATA/",p,"/10x/aggregation_csv.csv")) if (cellranger==2){
sc10x.aggr <- read_csv(paste0("./analysis/DATA/",p,"/10x/aggregation_csv.csv"))
} else {
sc10x.aggr <- read_csv(paste0("./analysis/DATA/",p,"/10x/aggregation.csv"))
}
} }
cell.codes <- as.data.frame(sc10x@raw.data@Dimnames[[2]]) cell.codes <- as.data.frame(sc10x@raw.data@Dimnames[[2]])
colnames(cell.codes) <- "barcodes" colnames(cell.codes) <- "barcodes"
......
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