Commit ebaa08e5 authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Create h5ad's after id

parent 33b034b3
......@@ -60,7 +60,7 @@ if (opt$o == "pr" && opt$s == "hu"){
rm(ref)
}
sc10x <- readRDS("./analysis/sc10x.raw.rds")
sc10x <- readRDS(paste0("./analysis/",opt$p,".raw.rds"))
sc10x.se <- as.SingleCellExperiment(sc10x)
common <- intersect(rownames(sc10x.se),rownames(lin.se))
......@@ -222,8 +222,21 @@ rm(list=ls(pattern="^sc10x.se"))
#scShinyOutput(sc10x.st,anal="id.st")
#scShinyOutput(sc10x.leu,anal="id.leu")
save(list=ls(pattern="^singler"),file='./analysis/singler_objects.RData')
save(list=ls(pattern="^sc10x"),file='./analysis/sc10x.id.rda')
save(list=ls(pattern="^sc10x.epi"),file='./analysis/sc10x.epi.id.rda')
save(list=ls(pattern="^sc10x.st"),file='./analysis/sc10x.st.id.rda')
#save.image(file="./analysis/sc10x.id.RData")
library(sceasy)
library(reticulate)
use_condaenv('sceasy')
convertFormat(sc10x,from="seurat",to="anndata",outFile=paste0("/project/urology/Strand_lab/shared/cellxgene/anndata/",opt$p,"_id_all.h5ad"),assay="SCT",main_layer="scale.data")
convertFormat(sc10x.epi,from="seurat",to="anndata",outFile=paste0("/project/urology/Strand_lab/shared/cellxgene/anndata/",opt$p,"_id_epi.h5ad"),assay="SCT",main_layer="scale.data")
convertFormat(sc10x.fmst,from="seurat",to="anndata",outFile=paste0("/project/urology/Strand_lab/shared/cellxgene/anndata/",opt$p,"_id_fmst.h5ad"),assay="SCT",main_layer="scale.data")
convertFormat(sc10x.leu,from="seurat",to="anndata",outFile=paste0("/project/urology/Strand_lab/shared/cellxgene/anndata/",opt$p,"_id_leu.h5ad"),assay="SCT",main_layer="scale.data")
saveRDS(sc10x,paste0("/project/urology/Strand_lab/shared/cellxgene/seurat/",opt$p,"_id_all.rds"))
saveRDS(sc10x.epi,paste0("/project/urology/Strand_lab/shared/cellxgene/seurat/",opt$p,"_id_epi.rds"))
saveRDS(sc10x.fmst,paste0("/project/urology/Strand_lab/shared/cellxgene/seurat/",opt$p,"_id_fmst.rds"))
saveRDS(sc10x.leu,paste0("/project/urology/Strand_lab/shared/cellxgene/seurat/",opt$p,"_id_leu.rds"))
......@@ -196,4 +196,4 @@ library(sceasy)
library(reticulate)
use_condaenv('sceasy')
convertFormat(sc10x,from="seurat",to="anndata",outFile=paste0("/project/urology/Strand_lab/shared/cellxgene/anndata/",project.name,"_raw.h5ad"),assay="SCT",main_layer="scale.data")
saveRDS(sc10x,paste0("/project/urology/Strand_lab/shared/cellxgene/seurat/",project.name,"_raw.rds"))
\ No newline at end of file
saveRDS(sc10x,paste0("/project/urology/Strand_lab/shared/cellxgene/seurat/",project.name,"_raw.rds"))
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