R/write_count.R

In miaozhun/ImputeSingle: scRecover for imputation of single-cell RNA-seq data

write_count <-
function (count_imp, filetype, out_dir, type, genelen) 
{
    totalCounts_by_cell = readRDS(paste0(out_dir, "totalCounts_by_cell.rds"))
    count_imp = sweep(count_imp, MARGIN = 2, totalCounts_by_cell/10^6, 
        FUN = "*")
    if(type == "TPM"){
      count_imp = sweep(count_imp, 1, genelen, FUN = "/")
    }
    count_imp = round(count_imp, digits = 2)
    if (filetype == "csv") {
        write.csv(count_imp, file = paste0(out_dir, "scimpute_count.csv"))
    }
    else if (filetype == "txt") {
        write.table(count_imp, file = paste0(out_dir, "scimpute_count.txt"), 
            quote = FALSE)
    }else if (filetype == "rds") {
        saveRDS(count_imp, file = paste0(out_dir, "scimpute_count.rds"))
    }else {
        print("filetype can be 'csv', 'txt', or 'rds'!")
        stop()
    }
    return(0)
}