importSEQC {singleCellTK} | R Documentation

## Construct SCE object from seqc output

### Description

Read the filtered barcodes, features, and matrices for all samples from (preferably a single run of) seqc output. Import and combine them as one big SingleCellExperiment object.

### Usage

    importSEQC(
      seqcDirs = NULL,
      samples = NULL,
      prefix = NULL,
      gzipped = FALSE,
      class = c("Matrix", "matrix"),
      delayedArray = TRUE,
      cbNotFirstCol = TRUE,
      feNotFirstCol = TRUE,
      combinedSample = TRUE
    )

### Arguments

`seqcDirs` | A vector of paths to seqc output files. Each sample should have its own path. For example: `./pbmc_1k_50x50`. Must have the same length as `samples`.
`samples` | A vector of user-defined sample names for the samples to be imported. Must have the same length as `seqcDirs`.
`prefix` | A vector containing the prefix of file names within each sample directory. It cannot be null and the vector should have the same length as samples.
`gzipped` | Boolean. `TRUE` if the seqc output files (sparse_counts_barcode.csv, sparse_counts_genes.csv, and sparse_molecule_counts.mtx) were gzip compressed. `FALSE` otherwise. Default seqc outputs are not gzipped. Default `FALSE`.
`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`.
`cbNotFirstCol` | Boolean. `TRUE` if first column of sparse_counts_barcode.csv is row index and it will be removed. `FALSE` the first column will be kept.
`feNotFirstCol` | Boolean. `TRUE` if first column of sparse_counts_genes.csv is row index and it will be removed. `FALSE` the first column will be kept.
`combinedSample` | Boolean. If `TRUE`, `importSEQC` returns a `SingleCellExperiment` object containing the combined count matrix, feature annotations and the cell annotations. If `FALSE`, `importSEQC` returns a list containing multiple `SingleCellExperiment` objects. Each `SingleCellExperiment` contains count matrix, feature annotations and cell annotations for each sample.

### Details

`importSEQC` imports output from seqc. The default sparse_counts_barcode.csv or sparse_counts_genes.csv from seqc output contains two columns. The first column is row index and the second column is cell-barcode or gene symbol. `importSEQC` will remove first column. Alternatively, user can call `cbNotFirstCol` or `feNotFirstCol` as FALSE to keep the first column of these files. When `combinedSample` is TRUE, `importSEQC` will combined count matrix with genes detected in at least one sample.

### Value

A `SingleCellExperiment` object containing the combined count matrix, the feature annotations, and the cell annotation.

### Examples

    # Example #1
    # The following filtered feature, cell, and matrix files were downloaded from
    # https://support.10xgenomics.com/single-cell-gene-expression/datasets/
    # 3.0.0/pbmc_1k_v3
    # The top 50 hg38 genes are included in this example.
    # Only the top 50 cells are included.
    sce <- importSEQC(
        seqcDirs = system.file("extdata/pbmc_1k_50x50", package = "singleCellTK"),
        samples = "pbmc_1k_50x50",
        prefix = "pbmc_1k",
        combinedSample = FALSE)

[Package singleCellTK version 2.0.0 Index]