importSTARsolo: Construct SCE object from STARsolo outputs

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

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 = c("Gene", "GeneFull"),
  matrixFileNames = "matrix.mtx",
  featuresFileNames = "features.tsv",
  barcodesFileNames = "barcodes.tsv",
  gzipped = "auto",
  class = c("Matrix", "matrix"),
  delayedArray = FALSE,
  rowNamesDedup = 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. The intermediate folder to filtered or raw cell barcode, feature, and matrix files for each of samples. Default "Gene". It can be either Gene or GeneFull as the main folder from which data needs to be imported.
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 FALSE.
rowNamesDedup	Boolean. Whether to deduplicate rownames. 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")

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.