suppressMessages(library(data.table))

library(Matrix)

args <- commandArgs(trailingOnly = TRUE)

devtools::load_all(args[1])

input.file <- paste0(getwd(), "/raw_data/pancreas/celseq.csv.gz")

raw.data <- suppressWarnings(expr = fread(

cmd = paste0("gzip -dc ", input.file),

data.table = FALSE,

fill = FALSE,

showProgress = FALSE)

)

rownames(raw.data) <- raw.data[, 1]

raw.data <- raw.data[, -1]

rownames(raw.data) <- make.unique(sapply(X = rownames(raw.data), FUN = function(x) {

Seurat:::ExtractField(string = x, field = 1, delim = "__")

}))

seurat.object <- CreateSeuratObject(counts = raw.data, project = "CELSEQ")

seurat.object <- subset(x = seurat.object, subset = nFeature_RNA > 1750)

seurat.object <- NormalizeData(object = seurat.object, verbose = FALSE)

seurat.object <- FindVariableFeatures(object = seurat.object, verbose = FALSE,

selection.method = "vst", nfeatures = 2000)

seurat.object[["tech"]] <- "celseq"

seurat.object[["replicate"]] <- "celseq"

Idents(object = seurat.object) <- "tech"

saveRDS(object = seurat.object, file = args[2])