importSTARsolo {singleCellTK} | R Documentation

## Construct SCE object from STARsolo outputs

### Description

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

### Usage

    importSTARsolo(
      STARsoloDirs,
      samples,
      STARsoloOuts = "Gene/filtered",
      matrixFileNames = "matrix.mtx",
      featuresFileNames = "features.tsv",
      barcodesFileNames = "barcodes.tsv",
      gzipped = "auto",
      class = c("Matrix", "matrix"),
      delayedArray = TRUE
    )

### Arguments

`STARsoloDirs` | A vector of root directories of STARsolo output files. The paths should be something like this: /PATH/TO/prefixSolo.out. For example: `./Solo.out`. Each sample 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 `STARsoloDirs`.
`STARsoloOuts` | Character vector. The intermediate paths to filtered or raw cell barcode, feature, and matrix files for each of `samples`. Default `"Gene/filtered"` which works for STAR 2.7.3a. Must have length 1 or the same length as `samples`.
`matrixFileNames` | Filenames for the Market Exchange Format (MEX) sparse matrix file (.mtx file). Must have length 1 or the same length as `samples`.
`featuresFileNames` | Filenames for the feature annotation file. Must have length 1 or the same length as `samples`.
`barcodesFileNames` | Filenames for the cell barcode list file. Must have length 1 or the same length as `samples`.
`gzipped` | Boolean. `TRUE` if the STARsolo output files (barcodes.tsv, features.tsv, and matrix.mtx) were gzip compressed. `FALSE` otherwise. This is `FALSE` in STAR 2.7.3a. Default `"auto"` which automatically detects if the files are gzip compressed. Must have length 1 or the same length as `samples`.
`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

    # Example #1
    # FASTQ files were downloaded from
    # https://support.10xgenomics.com/single-cell-gene-expression/datasets/3.0.0
    # /pbmc_1k_v3
    # They were concatenated as follows:
    # cat pbmc_1k_v3_S1_L001_R1_001.fastq.gz pbmc_1k_v3_S1_L002_R1_001.fastq.gz >
    # pbmc_1k_v3_R1.fastq.gz
    # cat pbmc_1k_v3_S1_L001_R2_001.fastq.gz pbmc_1k_v3_S1_L002_R2_001.fastq.gz >
    # pbmc_1k_v3_R2.fastq.gz
    # The following STARsolo command generates the filtered feature, cell, and
    # matrix files
    # STAR \
    #   --genomeDir ./index \
    #   --readFilesIn ./pbmc_1k_v3_R2.fastq.gz \
    #                 ./pbmc_1k_v3_R1.fastq.gz \
    #   --readFilesCommand zcat \
    #   --outSAMtype BAM Unsorted \
    #   --outBAMcompression -1 \
    #   --soloType CB_UMI_Simple \
    #   --soloCBwhitelist ./737K-august-2016.txt \
    #   --soloUMIlen 12

    # The top 20 genes and the first 20 cells are included in this example.
    sce <- importSTARsolo(
      STARsoloDirs = system.file("extdata/STARsolo_PBMC_1k_v3_20x20",
        package = "singleCellTK"),
      samples = "PBMC_1k_v3_20x20")

[Package singleCellTK version 2.0.0 Index]