CellTypeMarkers: Cell-type markers

In acidgenomics/r-acidsinglecell: Acid Genomics Single Cell Experiment

Cell-type markers

Description

Cell-type markers

Usage

CellTypeMarkers(object, geneToSymbol)

importCellTypeMarkers(file, organism, release, ignoreVersion = TRUE)

Arguments

object	Object.
geneToSymbol	GeneToSymbol. Gene-to-symbol mappings. Must contain geneId and geneName columns. See GeneToSymbol for more information.
file	character(1). File path.
organism	character(1). Full Latin organism name (e.g. "Homo sapiens").
release	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.
ignoreVersion	logical(1). Ignore identifier (e.g. transcript, gene) versions. When applicable, the identifier containing version numbers will be stored in txIdVersion and geneIdVersion, and the variants without versions will be stored in txId, txIdNoVersion, geneId, and geneIdNoVersion.

Value

CellTypeMarkers.

Note

Updated 2024-03-27.

Examples

markersDir <- system.file(
    "extdata", "markers",
    package = "AcidSingleCell"
)
cellTypeDir <- file.path(markersDir, "cell-type")
files <- sort(list.files(
    path = cellTypeDir,
    pattern = "*.csv",
    full.names = TRUE
))
file <- files[[1L]]
organism <- syntactic::sentenceCase(
    gsub(
        pattern = "-",
        replacement = " ",
        x = AcidBase::basenameSansExt(file)
    )
)
releaseFile <- file.path(markersDir, "ensembl-release.txt")
release <- as.integer(readLines(releaseFile))
object <- importCellTypeMarkers(
    file = file,
    organism = organism,
    release = release
)
print(object)

acidgenomics/r-acidsinglecell documentation built on March 30, 2024, 5:39 a.m.