Commit 1179ce77 authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Set SingleR project name by cli

parent 4dce7aea
......@@ -14,4 +14,4 @@ source activate umap
module load R/3.5.1-gccmkl
module load hdf5_18/1.8.17
Rscript ../r.scripts/SingleR.R
Rscript ../r.scripts/SingleR.R --p "$1" --s "$2"
......@@ -36,7 +36,7 @@ load("./analysis/sc10x.raw.RData")
load("./genesets/scDWS.250.rda")
load("./genesets/cibersort.rda")
singler = CreateBigSingleRObject(GetAssayData(sc10x,assay="SCT"), annot = NULL, "PdPbPc", min.genes = 0,
singler = CreateBigSingleRObject(GetAssayData(sc10x,assay="SCT"), annot = NULL, opt$p, min.genes = 0,
technology = "10X", species = "Human", citation = "",
ref.list = list(scDWS.250), normalize.gene.length = F, variable.genes = "de",
fine.tune = T, do.signatures = T, clusters = NULL, do.main.types = F,
......@@ -129,7 +129,7 @@ for (i in c("epi","fmst","st","leu")){
dev.off()
}
singler.leu = CreateSinglerObject(GetAssayData(sc10x.leu,assay="SCT"), annot = NULL, "PdPbPc", min.genes = 0,
singler.leu = CreateSinglerObject(GetAssayData(sc10x.leu,assay="SCT"), annot = NULL, opt$p, min.genes = 0,
technology = "10X", species = "Human", citation = "",
ref.list = list(cibersort), normalize.gene.length = F, variable.genes = "de",
fine.tune = T, do.signatures = T, clusters = NULL, do.main.types = T,
......
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