Read the barcodes, features (genes), and matrices from STARsolo outputs. Import them as one SingleCellExperiment object.
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
.
A vector of user-defined sample names for the sample to be
imported. Must have the same length as STARsoloDirs
.
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.
Filenames for the Market Exchange Format (MEX) sparse
matrix file (.mtx file). Must have length 1 or the same
length as samples
.
Filenames for the feature annotation file.
Must have length 1 or the same
length as samples
.
Filenames for the cell barcode list file.
Must have length 1 or the same
length as samples
.
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
.
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".
Boolean. Whether to read the expression matrix as
DelayedArray object or not. Default FALSE
.
Boolean. Whether to deduplicate rownames. 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")
#> Metrics summary file (Summary.csv) not found for sample: PBMC_1k_v3_20x20