bcbioSingleCell: 'bcbioSingleCell' Object and Constructor
In WeiSong-bio/roryk-bcbioSinglecell: Single-Cell RNA-Seq Utilities

Description Usage Arguments Value Remote Data Note Author(s) See Also Examples

bcbioSingleCell is an S4 class that extends SingleCellExperiment, and is designed to store a bcbio single-cell RNA-seq analysis. This class contains read counts saved as a sparse matrix (dgCMatrix), sample metadata, and cell quality control metrics.

bcbioSingleCell(uploadDir, organism = NULL, sampleMetadataFile = NULL,
  interestingGroups = "sampleName", ensemblRelease = NULL,
  genomeBuild = NULL, transgeneNames = NULL, spikeNames = NULL,
  gffFile = NULL, ...)

`uploadDir`	Path to final upload directory. This path is set when running "`bcbio_nextgen -w template`".
`organism`	Organism name. Use the full latin name (e.g. "Homo sapiens"), since this will be input downstream to AnnotationHub and ensembldb, unless `gffFile` is set.
`sampleMetadataFile`	Sample barcode metadata file. Optional for runs with demultiplixed index barcodes (e.g. SureCell), but otherwise required for runs with multipliexed FASTQs containing multiple index barcodes (e.g. inDrop).
`interestingGroups`	Character vector of interesting groups. Must be formatted in camel case and intersect with `sampleData()` colnames.
`ensemblRelease`	Optional. Ensembl release version. If `NULL`, defaults to current release, and does not typically need to be user-defined. Passed to AnnotationHub for `EnsDb` annotation matching, unless `gffFile` is set.
`genomeBuild`	Optional. Ensembl genome build name (e.g. "GRCh38"). This will be passed to AnnotationHub for `EnsDb` annotation matching, unless `gffFile` is set.
`transgeneNames`	`character` vector indicating which `assay()` rows denote transgenes (e.g. EGFP, TDTOMATO).
`spikeNames`	`character` vector indicating which `assay()` rows denote spike-in sequences (e.g. ERCCs).
`gffFile`	Optional, not recommended. By default, we recommend leaving this `NULL` for genomes that are supported on Ensembl. In this case, the row annotations (`rowRanges()`) will be obtained automatically from Ensembl by passing the `organism`, `genomeBuild`, and `ensemblRelease` arguments to AnnotationHub and ensembldb. For a genome that is not supported on Ensembl and/or AnnotationHub, a GFF/GTF (General Feature Format) file is required. Generally, we recommend using a GTF (GFFv2) file here over a GFF3 file if possible, although all GFF formats are supported. The function will internally generate a `TxDb` containing transcript-to-gene mappings and construct a `GRanges` object containing the genomic ranges (`rowRanges()`).
`...`	Additional arguments, to be stashed in the `metadata()` slot.

bcbioSingleCell.

When working in RStudio, we recommend connecting to the bcbio-nextgen run directory as a remote connection over sshfs.

bcbioSingleCell extended SummarizedExperiment prior to v0.1.0, where we migrated to SingleCellExperiment.

Michael Steinbaugh, Rory Kirchner

SingleCellExperiment::SingleCellExperiment().
.S4methods(class = "bcbioSingleCell").

Other S4 Object: coerce, extract, show, updateObject

uploadDir <- system.file("extdata/indrops", package = "bcbioSingleCell")
x <- bcbioSingleCell(
    uploadDir = uploadDir,
    organism = "Homo sapiens",
    sampleMetadataFile = file.path(uploadDir, "metadata.csv"),
    ensemblRelease = 87L
)
show(x)
validObject(x)