importSTARsolo: Construct SCE object from STARsolo outputs
In singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Description Usage Arguments Value Examples

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

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

`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`.

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

# 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")