#' Single-cell RNA sequencing and proteomics
#'
#' @description SCoPE2 assembles data on-the-fly from `ExperimentHub` to provide
#' a
#' [`MultiAssayExperiment`][MultiAssayExperiment::MultiAssayExperiment-class]
#' container. The `DataType` argument provides access to the `SCoPE2` dataset
#' as provided by Specht et al. (2020; DOI:
#' <http://dx.doi.org/10.1101/665307>). The article provides more information
#' about the data acquisition and pre-processing.
#'
#' @details The SCoPE2 study combines scRNA-seq (transcriptome) and
#' single-cell proteomics.
#'
#' * macrophage_differentiation: the cells are monocytes that undergo
#' macrophage differentiation. No annotation is available for the
#' transcriptome data, but batch and cell type annotations are
#' available for the proteomics data in the `celltype` `colData` column.
#' The transcriptomics and proteomics data were not measured from the same
#' cells but from a distinct set of cell cultures.
#' This dataset provides already filtered bad quality cells.
#' * scRNAseq1 - single-cell transcriptome (batch 1)
#' * scRNAseq2 - single-cell transcriptome (batch 2)
#' * scp - single-cell proteomics
#'
#' @inheritParams scNMT
#'
#' @param DataType `character(1)` Indicates study that produces this type of
#' data (default: 'macrophage_differentiation')
#'
#' @param modes `character()` A wildcard / glob pattern of modes, such as
#' `"rna"`. A wildcard of `"*"` will return all modes, that are
#' transcriptome ("rna") or proteome ("protein") which is the
#' default.
#'
#' @param version `character(1)`, currently only version '1.0.0' is
#' available
#'
#' @return A single cell multi-modal
#' [`MultiAssayExperiment`][MultiAssayExperiment::MultiAssayExperiment-class]
#' or informative `data.frame` when `dry.run` is `TRUE`
#'
#' @seealso SingleCellMultiModal-package
#'
#' @source All files are linked from the slavovlab website
#' <https://scope2.slavovlab.net/docs/data>
#'
#' @references
#' Specht, Harrison, Edward Emmott, Aleksandra A. Petelski, R.
#' Gray Huffman, David H. Perlman, Marco Serra, Peter Kharchenko,
#' Antonius Koller, and Nikolai Slavov. 2020. “Single-Cell
#' Proteomic and Transcriptomic Analysis of Macrophage
#' Heterogeneity.” bioRxiv. https://doi.org/10.1101/665307.
#'
#' @examples
#'
#' SCoPE2(DataType = "macrophage_differentiation",
#' modes = "*",
#' version = "1.0.0",
#' dry.run = TRUE)
#'
#' @export
SCoPE2 <- function(
DataType = "macrophage_differentiation",
modes = "*",
version = "1.0.0",
dry.run = TRUE,
verbose = TRUE,
...
) {
if (version != "1.0.0")
stop("Only version '1.0.0' is available.")
## Retrieve the different resources from ExperimentHub
ess_list <- .getResourcesList(
prefix = "macrophage_",
datatype = DataType,
modes = modes,
version = version,
dry.run = dry.run,
verbose = verbose,
...
)
## If dry.run, return only the information table
if (dry.run) return(ess_list)
## Get the colData
cd <- .mergeLowColData(ess_list[["experiments"]])
colnames(cd)[which(colnames(cd) == "Batch")] <- "batch_Chromium"
## Construct and return the MAE object
MultiAssayExperiment(
experiments = ess_list[["experiments"]],
colData = cd
)
}
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