101_prepare_benchmarkdata_R.ipynb

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     "text": [
      "Loading required package: SummarizedExperiment\n",
      "\n",
      "Loading required package: GenomicRanges\n",
      "\n",
      "Loading required package: stats4\n",
      "\n",
      "Loading required package: BiocGenerics\n",
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      "Loading required package: parallel\n",
      "\n",
      "\n",
      "Attaching package: ‘BiocGenerics’\n",
      "\n",
      "\n",
      "The following objects are masked from ‘package:parallel’:\n",
      "\n",
      "    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\n",
      "    clusterExport, clusterMap, parApply, parCapply, parLapply,\n",
      "    parLapplyLB, parRapply, parSapply, parSapplyLB\n",
      "\n",
      "\n",
      "The following objects are masked from ‘package:stats’:\n",
      "\n",
      "    IQR, mad, sd, var, xtabs\n",
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      "\n",
      "    Filter, Find, Map, Position, Reduce, anyDuplicated, append,\n",
      "    as.data.frame, basename, cbind, colnames, dirname, do.call,\n",
      "    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,\n",
      "    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,\n",
      "    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,\n",
      "    tapply, union, unique, unsplit, which, which.max, which.min\n",
      "\n",
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      "\n",
      "The following object is masked from ‘package:base’:\n",
      "\n",
      "    expand.grid\n",
      "\n",
      "\n",
      "Loading required package: IRanges\n",
      "\n",
      "Loading required package: GenomeInfoDb\n",
      "\n",
      "Loading required package: Biobase\n",
      "\n",
      "Welcome to Bioconductor\n",
      "\n",
      "    Vignettes contain introductory material; view with\n",
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      "    'citation(\"Biobase\")', and for packages 'citation(\"pkgname\")'.\n",
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      "\n",
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      "The following objects are masked from ‘package:base’:\n",
      "\n",
      "    aperm, apply, rowsum\n",
      "\n",
      "\n"
     ]
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   ],
   "source": [
    "library(SingleCellExperiment)\n",
    "library(MASS)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "data = readRDS('datasets/DuoClustering2018/sce_full/sce_full_Zhengmix8eq.rds')\n",
    "write.table(counts(data), file = \"datasets/DuoClustering2018/sce_full/sce_full_Zhengmix8eq.csv\",sep=\",\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
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   "outputs": [
    {
     "data": {
      "text/plain": [
       "class: SingleCellExperiment \n",
       "dim: 15716 3994 \n",
       "metadata(1): log.exprs.offset\n",
       "assays(3): counts logcounts normcounts\n",
       "rownames(15716): ENSG00000237683 ENSG00000228327 ... ENSG00000215700\n",
       "  ENSG00000215699\n",
       "rowData names(10): id symbol ... total_counts log10_total_counts\n",
       "colnames(3994): b.cells1147 b.cells6276 ... naive.t1167 naive.t4926\n",
       "colData names(14): dataset barcode ... libsize.drop feature.drop\n",
       "reducedDimNames(2): PCA TSNE\n",
       "spikeNames(0):\n",
       "altExpNames(0):"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
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   "source": [
    "data"
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