Read the filtered barcodes, features, and matrices for all samples from (preferably a single run of) Cell Ranger output. Import and combine them as one big SingleCellExperiment object.
importCellRanger(
cellRangerDirs = NULL,
sampleDirs = NULL,
sampleNames = NULL,
cellRangerOuts = NULL,
dataType = c("filtered", "raw"),
matrixFileNames = "matrix.mtx.gz",
featuresFileNames = "features.tsv.gz",
barcodesFileNames = "barcodes.tsv.gz",
gzipped = "auto",
class = c("Matrix", "matrix"),
delayedArray = FALSE,
rowNamesDedup = TRUE
)
importCellRangerV2(
cellRangerDirs = NULL,
sampleDirs = NULL,
sampleNames = NULL,
dataTypeV2 = c("filtered", "raw"),
class = c("Matrix", "matrix"),
delayedArray = FALSE,
reference = NULL,
cellRangerOutsV2 = NULL,
rowNamesDedup = TRUE
)
importCellRangerV3(
cellRangerDirs = NULL,
sampleDirs = NULL,
sampleNames = NULL,
dataType = c("filtered", "raw"),
class = c("Matrix", "matrix"),
delayedArray = FALSE,
rowNamesDedup = TRUE
)The root directories where Cell Ranger was run. These
folders should contain sample specific folders. Default NULL,
meaning the paths for each sample will be specified in samples
argument.
Default NULL. Can be one of
NULL. All samples within cellRangerDirs will be
imported. The order of samples will be first determined by the order of
cellRangerDirs and then by list.dirs. This is only
for the case where cellRangerDirs is specified.
A list of vectors containing the folder names for samples to import.
Each vector in
the list corresponds to samples from one of cellRangerDirs.
These names are the same as the folder names under cellRangerDirs.
This is only for the case where cellRangerDirs is specified.
A vector of folder paths for the samples to import. This is only for
the case where cellRangerDirs is NULL.
The cells in the final SCE object will be ordered in the same order of
sampleDirs.
A vector of user-defined sample names for the samples
to be
imported. Must have the same length as length(unlist(sampleDirs)) if
sampleDirs is not NULL. Otherwise, make sure the length and
order match the output of
unlist(lapply(cellRangerDirs, list.dirs, recursive = FALSE)). Default
NULL, in which case the folder names will be used as sample names.
Character vector. The intermediate
paths to filtered or raw cell barcode, feature, and matrix files
for each sample. Supercedes dayaType. If NULL,
dataType
will be used to determine Cell Ranger output directory. If not NULL,
dataType will be ingored and cellRangerOuts specifies the
paths. Must have length 1 or the same length as
length(unlist(sampleDirs)) if
sampleDirs is not NULL. Otherwise, make sure the length and
order match the output of
unlist(lapply(cellRangerDirs, list.dirs, recursive = FALSE)).
Reference genome names might need to be
appended for CellRanger version below 3.0.0 if reads were mapped to
multiple genomes when running Cell Ranger pipeline. Probable options
include "outs/filtered_feature_bc_matrix/", "outs/raw_feature_bc_matrix/",
"outs/filtered_gene_bc_matrix/", "outs/raw_gene_bc_matrix/".
Character. The type of data to import. Can be one of
"filtered" (which is equivalent to
cellRangerOuts = "outs/filtered_feature_bc_matrix/" or
cellRangerOuts = "outs/filtered_gene_bc_matrix/") or "raw" (which
is equivalent to
cellRangerOuts = "outs/raw_feature_bc_matrix/" or
cellRangerOuts = "outs/raw_gene_bc_matrix/"). Default
"filtered" which imports the counts for filtered cell barcodes only.
Character vector. Filenames for the Market Exchange
Format (MEX) sparse matrix files (matrix.mtx or matrix.mtx.gz files).
Must have length 1 or the same
length as length(unlist(sampleDirs)) if
sampleDirs is not NULL. Otherwise, make sure the length and
order match the output of
unlist(lapply(cellRangerDirs, list.dirs, recursive = FALSE)).
Character vector. Filenames for the feature
annotation files. They are usually named features.tsv.gz or
genes.tsv. Must have length 1 or the same
length as length(unlist(sampleDirs)) if
sampleDirs is not NULL. Otherwise, make sure the length and
order match the output of
unlist(lapply(cellRangerDirs, list.dirs, recursive = FALSE)).
Character vector. Filename for the cell barcode
list files. They are usually named barcodes.tsv.gz or
barcodes.tsv. Must have length 1 or the same
length as length(unlist(sampleDirs)) if
sampleDirs is not NULL. Otherwise, make sure the length and
order match the output of
unlist(lapply(cellRangerDirs, list.dirs, recursive = FALSE)).
TRUE if the Cell Ranger output files
(barcodes.tsv, features.tsv, and matrix.mtx) were
gzip compressed. FALSE otherwise. This is true after Cell Ranger
3.0.0 update. Default "auto" which automatically detects if the
files are gzip compressed. If not "auto", gzipped must have
length 1 or the same
length as length(unlist(sampleDirs)) if
sampleDirs is not NULL. Otherwise, make sure the length and
order match the output of
unlist(lapply(cellRangerDirs, list.dirs, recursive = FALSE)).
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.
Character. The type of output to import for
Cellranger version below 3.0.0. Whether to import the filtered or the
raw data. Can be one of 'filtered' or 'raw'. Default 'filtered'. When
cellRangerOuts is specified, dataTypeV2 and reference will
be ignored.
Character vector. The reference genome names.
Default NULL. If not NULL, it must gave the length and order as
length(unlist(sampleDirs)) if sampleDirs is not NULL.
Otherwise, make sure the length and order match the output of
unlist(lapply(cellRangerDirs, list.dirs, recursive = FALSE)). Only needed
for Cellranger version below 3.0.0.
Character vector. The intermediate paths
to filtered or raw cell barcode, feature, and matrix files for each
sample for Cellranger version below 3.0.0. If NULL, reference and
dataTypeV2 will be used to determine Cell Ranger output directory. If it has
length 1, it assumes that all samples use the same genome reference and
the function will load only filtered or raw data.
A SingleCellExperiment object containing the combined count
matrix, the feature annotations, and the cell annotation.
importCellRangerV2 imports output from Cell Ranger V2.
importCellRangerV2Sample imports output from one sample from Cell
Ranger V2.
importCellRangerV3 imports output from Cell Ranger V3.
importCellRangerV3 imports output from one sample from Cell Ranger
V3.
Some implicit
assumptions which match the output structure of Cell Ranger V2 & V3
are made in these 4 functions including cellRangerOuts,
matrixFileName, featuresFileName, barcodesFileName,
and gzipped.
Alternatively, user can call importCellRanger to explicitly
specify these arguments.
# 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/hgmm_1k_v3
# The top 10 hg19 & mm10 genes are included in this example.
# Only the first 20 cells are included.
sce <- importCellRanger(
cellRangerDirs = system.file("extdata/", package = "singleCellTK"),
sampleDirs = "hgmm_1k_v3_20x20",
sampleNames = "hgmm1kv3",
dataType = "filtered")
#> Metrics summary file (metrics_summary.csv) not found for sample: hgmm1kv3
# The following filtered feature, cell, and matrix files were downloaded from
# https://support.10xgenomics.com/single-cell-gene-expression/datasets/
# 2.1.0/pbmc4k
# Top 20 genes are kept. 20 cell barcodes are extracted.
sce <- importCellRangerV2(
cellRangerDirs = system.file("extdata/", package = "singleCellTK"),
sampleDirs = "pbmc_4k_v2_20x20",
sampleNames = "pbmc4k_20",
reference = 'GRCh38',
dataTypeV2 = "filtered")
#> Metrics summary file (metrics_summary.csv) not found for sample: pbmc4k_20
sce <- importCellRangerV3(
cellRangerDirs = system.file("extdata/", package = "singleCellTK"),
sampleDirs = "hgmm_1k_v3_20x20",
sampleNames = "hgmm1kv3",
dataType = "filtered")
#> Metrics summary file (metrics_summary.csv) not found for sample: hgmm1kv3