CellRanger: Cell Ranger RNA-seq data set

In steinbaugh/Chromium: 10X Genomics Chromium

Cell Ranger RNA-seq data set

Description

Contains UMI droplet-based single-cell RNA-seq data.

Usage

CellRanger(
  dir,
  filtered = TRUE,
  organism = NULL,
  ensemblRelease = NULL,
  genomeBuild = NULL,
  gffFile = NULL,
  refdataDir = NULL,
  samples = NULL,
  censorSamples = NULL,
  sampleMetadataFile = NULL,
  transgeneNames = NULL,
  interestingGroups = "sampleName"
)

Arguments

dir	character(1). Directory path to Cell Ranger output.
filtered	logical(1). Use filtered (recommended) or raw counts. Note that raw counts still contain only whitelisted cellular barcodes.
organism	character(1). Full Latin organism name (e.g. "Homo sapiens").
ensemblRelease	integer(1). Ensembl release version (e.g. 100). We recommend setting this value if possible, for improved reproducibility. When left unset, the latest release available via AnnotationHub/ensembldb is used. Note that the latest version available can vary, depending on the versions of AnnotationHub and ensembldb in use.
genomeBuild	character(1). Ensembl genome build assembly name (e.g. "GRCh38"). If set NULL, defaults to the most recent build available. Note: don't pass in UCSC build IDs (e.g. "hg38").
gffFile	character(1). GFF/GTF (General Feature Format) file. Generally, we recommend using GTF (GFFv2) instead of GFFv3.
refdataDir	character(1) or NULL. Directory path to Cell Ranger reference annotation data.
samples	character. Sample identifiers.
censorSamples	character. Specify a subset of samples to censor.
sampleMetadataFile	character(1). Sample metadata file path. CSV or TSV is preferred, but Excel worksheets are also supported. Check the documentation for conventions and required columns.
transgeneNames	character. Vector indicating which assay rows denote transgenes (e.g. EGFP, TDTOMATO).
interestingGroups	character. Groups of interest to use for visualization. Corresponds to factors describing the columns of the object.

Details

Read 10x Genomics Cell Ranger output for a Chromium data set into a SingleCellExperiment object.

Currently supports loading of a single genome.

Value

CellRanger.

Directory structure for multiple samples

Cell Ranger can vary in its output directory structure, but we're requiring a single, consistent directory structure for datasets containing multiple samples that have not been aggregated into a single matrix with aggr.

Cell Ranger v3 output:

| <dir>/
|-- <sampleName>/
|---- SC_RNA_COUNTER_CS/
|---- outs/
|------ filtered_feature_bc_matrix/
|-------- barcodes.tsv.gz
|-------- features.tsv.gz
|-------- matrix.mtx.gz
|------ filtered_feature_bc_matrix.h5
|------ metrics_summary.csv
|------ molecule_info.h5
|------ possorted_genome_bam.bam
|------ possorted_genome_bam.bam.bai
|------ raw_feature_bc_matrix/
|-------- barcodes.tsv.gz
|-------- features.tsv.gz
|-------- matrix.mtx.gz
|------ raw_feature_bc_matrix.h5
|------ web_summary.html

Cell Ranger v2 output:

| <dir>/
|-- <sampleName>/
|---- SC_RNA_COUNTER_CS/
|---- outs/
|------ filtered_gene_bc_matrices/
|-------- <genomeBuild>/
|---------- barcodes.tsv
|---------- genes.tsv
|---------- matrix.mtx
|------ filtered_gene_bc_matrices_h5.h5
|------ metrics_summary.csv
|------ molecule_info.h5
|------ possorted_genome_bam.bam
|------ possorted_genome_bam.bam.bai
|------ raw_gene_bc_matrices/
|-------- <genomeBuild>/
|---------- barcodes.tsv
|---------- genes.tsv
|---------- matrix.mtx
|------ raw_gene_bc_matrices_h5.h5

Sample metadata

A user-supplied sample metadata file defined by sampleMetadataFile is required for multiplexed datasets. Otherwise this can be left NULL, and minimal sample data will be used, based on the directory names.

Reference data

We strongly recommend supplying the corresponding reference data required for Cell Ranger with the refdataDir argument. It will convert the gene annotations defined in the GTF file into a GRanges object, which get slotted in rowRanges(). Otherwise, the function will attempt to use the most current annotations available from Ensembl, and some gene IDs may not match, due to deprecation in the current Ensembl release.

Note

Updated 2022-06-07.

See Also

• https://support.10xgenomics.com/single-cell-gene-expression/

Examples

dir <- system.file("extdata", "cellranger_v3", package = "Chromium")
x <- CellRanger(dir)
print(x)

steinbaugh/Chromium documentation built on Oct. 13, 2023, 4:17 p.m.