Read the barcodes, features (genes), and matrices from Optimus outputs. Import them as one SingleCellExperiment object.
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 = FALSE )
OptimusDirs | A vector of root directories of Optimus output files.
The paths should be something like this:
|
---|---|
samples | A vector of user-defined sample names for the sample to be
imported. Must have the same length as |
matrixLocation | Character. It is the intermediate
path to the filtered count maxtrix file saved in sparse matrix format
( |
colIndexLocation | Character. The intermediate path to the barcode
index file. Default |
rowIndexLocation | Character. The intermediate path to the feature
(gene) index file. Default
|
cellMetricsLocation | Character. It is the intermediate
path to the cell metrics file ( |
geneMetricsLocation | Character. It is the intermediate
path to the feature (gene) metrics file ( |
emptyDropsLocation | Character. It is the intermediate
path to emptyDrops metrics file
( |
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 |
A SingleCellExperiment object containing the count matrix, the gene annotation, and the cell annotation.
file.path <- system.file("extdata/Optimus_20x1000", package = "singleCellTK") if (FALSE) { sce <- importOptimus(OptimusDirs = file.path, samples = "Optimus_20x1000") }