importOptimus {singleCellTK} | R Documentation

## Construct SCE object from Optimus output

### Description

Read the barcodes, features (genes), and matrices from Optimus outputs. Import them as one SingleCellExperiment object.

### Usage

    importOptimus(
      OptimusDirs,
      samples,
      matrixLocation = "call-MergeCountFiles/sparse_counts.npz",
      colIndexLocation = "call-MergeCountFiles/sparse_counts_col_index.npy",
      rowIndexLocation = "call-MergeCountFiles/sparse_counts_row_index.npy",
      cellMetricsLocation = "call-MergeCellMetrics/merged-cell-metrics.csv.gz",
      geneMetricsLocation = "call-MergeGeneMetrics/merged-gene-metrics.csv.gz",
      emptyDropsLocation = "call-RunEmptyDrops/empty_drops_result.csv",
      class = c("Matrix", "matrix"),
      delayedArray = TRUE
    )

### Arguments

`OptimusDirs` | A vector of root directories of Optimus output files. The paths should be something like this: `/PATH/TO/bb4a2a5e-ff34-41b6-97d2-0c0c0c534530`. Each entry in `OptimusDirs` is considered a sample and should have its own path. Must have the same length as `samples`.
`samples` | A vector of user-defined sample names for the sample to be imported. Must have the same length as `OptimusDirs`.
`matrixLocation` | Character. It is the intermediate path to the filtered count maxtrix file saved in sparse matrix format (`.npz`). Default `call-MergeCountFiles/sparse_counts.npz` which works for optimus_v1.4.0.
`colIndexLocation` | Character. The intermediate path to the barcode index file. Default `call-MergeCountFiles/sparse_counts_col_index.npy`.
`rowIndexLocation` | Character. The intermediate path to the feature (gene) index file. Default `call-MergeCountFiles/sparse_counts_row_index.npy`.
`cellMetricsLocation` | Character. It is the intermediate path to the cell metrics file (`merged-cell-metrics.csv.gz`). Default `call-MergeCellMetrics/merged-cell-metrics.csv.gz` which works for optimus_v1.4.0.
`geneMetricsLocation` | Character. It is the intermediate path to the feature (gene) metrics file (`merged-gene-metrics.csv.gz`). Default `call-MergeGeneMetrics/merged-gene-metrics.csv.gz` which works for optimus_v1.4.0.
`emptyDropsLocation` | Character. It is the intermediate path to emptyDrops metrics file (`empty_drops_result.csv`). Default `call-RunEmptyDrops/empty_drops_result.csv` which works for optimus_v1.4.0.
`class` | Character. The class of the expression matrix stored in the SCE object. Can be one of "Matrix" (as returned by readMM function), or "matrix" (as returned by matrix function). Default "Matrix".
`delayedArray` | Boolean. Whether to read the expression matrix as DelayedArray object or not. Default `TRUE`.

### Value

A SingleCellExperiment object containing the count matrix, the gene annotation, and the cell annotation.

### Examples

    file.path <- system.file("extdata/Optimus_20x1000",
      package = "singleCellTK")
    ## Not run:
    sce <- importOptimus(OptimusDirs = file.path,
      samples = "Optimus_20x1000")

    ## End(Not run)

[Package singleCellTK version 2.0.0 Index]