R/data.R

In PelzKo/immunedeconv2: Second generation methods for immune cell deconvolution

#' Example RNA-seq dataset from Hoek et al.
#'
#' A dataset of eight RNA-seq samples from patients vaccinated with trivalent inactivated influenza
#' vaccine (TIV)
#'
#' @format matrix with genes x samples
#'
#' @source Hoek et al. (2015), PLOS ONE,
#'   https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118528
"bulk"

#' Gold standard measurements with FACS from Hoek et al.
#'
#' A dataset of cell-type fractions of eight RNA-seq samples measured with FACS
#'
#' @format matrix with samples x cell types
#'
#' @source Hoek et al. (2015), PLOS ONE,
#'   https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118528
"RefData"

#' Example single-cell RNA-seq dataset Number 1 from Hao et al.
#'
#' A subset of raw counts of single-cell RNA-seq gene expression, containing 2400 cells.
#' his contains no cells which are in the other two subsets and all genes with only 0's in
#' all cells are removed
#'
#' @format A matrix with 19007 genes as rows and 2400 cells as columns
#'
#' @source Hao et al. (2021): Integrated analysis of multimodal single-cell data.
#'   In Cell 184 (13), 3573-3587.e29. DOI: 10.1016/j.cell.2021.04.048.
"single_cell_data_1"

#' Example single-cell RNA-seq dataset Number 2 from Hao et al.
#'
#' A subset of raw counts of single-cell RNA-seq gene expression, containing 2400 cells.
#' his contains no cells which are in the other two subsets and all genes with only 0's in
#' all cells are removed
#'
#' @format A matrix with 19051 genes as rows and 2400 cells as columns
#'
#' @source Hao et al. (2021): Integrated analysis of multimodal single-cell data.
#'   In Cell 184 (13), 3573-3587.e29. DOI: 10.1016/j.cell.2021.04.048.
"single_cell_data_2"

#' Example single-cell RNA-seq dataset Number 3 from Hao et al.
#'
#' A subset of raw counts of single-cell RNA-seq gene expression, containing 2400 cells.
#' his contains no cells which are in the other two subsets and all genes with only 0's in
#' all cells are removed
#'
#' @format A matrix with 19131 genes as rows and 2400 cells as columns
#'
#' @source Hao et al. (2021): Integrated analysis of multimodal single-cell data.
#'   In Cell 184 (13), 3573-3587.e29. DOI: 10.1016/j.cell.2021.04.048.
"single_cell_data_3"

#' Cell Type Annotations Number 1 from Hao et al.
#'
#' The corresponding cell type annotations containing the classes
#'    "B", "CD4 T", "CD8 T", "DC", "Mono" and "NK"
#'
#' @format A vector with the annotations. In the same order as the columns
#'
#' @source Hao et al. (2021): Integrated analysis of multimodal single-cell data.
#'   In Cell 184 (13), 3573-3587.e29. DOI: 10.1016/j.cell.2021.04.048.
"cell_type_annotations_1"

#' Cell Type Annotations Number 2 from Hao et al.
#'
#' The corresponding cell type annotations containing the classes
#'    "B", "CD4 T", "CD8 T", "DC", "Mono" and "NK"
#'
#' @format A vector with the annotations. In the same order as the columns
#'
#' @source Hao et al. (2021): Integrated analysis of multimodal single-cell data.
#'   In Cell 184 (13), 3573-3587.e29. DOI: 10.1016/j.cell.2021.04.048.
"cell_type_annotations_2"

#' Cell Type Annotations Number 3 from Hao et al.
#'
#' The corresponding cell type annotations containing the classes
#'    "B", "CD4 T", "CD8 T", "DC", "Mono" and "NK"
#'
#' @format A vector with the annotations. In the same order as the columns
#'
#' @source Hao et al. (2021): Integrated analysis of multimodal single-cell data.
#'   In Cell 184 (13), 3573-3587.e29. DOI: 10.1016/j.cell.2021.04.048.
"cell_type_annotations_3"

#' Patient ids Number 1 from Hao et al.
#'
#' The identifiers of patients of whom the cells were taken
#'
#' @format A vector with the patient ids. In the same order as the columns
#'
#' @source Hao et al. (2021): Integrated analysis of multimodal single-cell data.
#'   In Cell 184 (13), 3573-3587.e29. DOI: 10.1016/j.cell.2021.04.048.
"batch_ids_1"

#' Patient ids Number 2 from Hao et al.
#'
#' The identifiers of patients of whom the cells were taken
#'
#' @format A vector with the patient ids. In the same order as the columns
#'
#' @source Hao et al. (2021): Integrated analysis of multimodal single-cell data.
#'   In Cell 184 (13), 3573-3587.e29. DOI: 10.1016/j.cell.2021.04.048.
"batch_ids_2"

#' Patient ids Number 3 from Hao et al.
#'
#' The identifiers of patients of whom the cells were taken
#'
#' @format A vector with the patient ids. In the same order as the columns
#'
#' @source Hao et al. (2021): Integrated analysis of multimodal single-cell data.
#'   In Cell 184 (13), 3573-3587.e29. DOI: 10.1016/j.cell.2021.04.048.
"batch_ids_3"