R/cytoHDBMW.R

In Ghoshlab/cytoKernel: Differential expression using kernel-based score test

#' Example of processed dimensionally reduced flow cytometry
#' (marker median intensities) Bodenmiller_BCR_XL_flowSet()
#' expression dataset from HDCytoData Bioconductor data package.
#' 
#' The raw data (fcs files) were pre-processed using
#' CATALYST, scuttle, scran Bioconductor packages and igraph
#' CRAN package.
#' The data processing package includes 4 steps and
#' they are as follows:
#' 1. Creating a SingleCellExperiment Object: the flowSet
#' data object along with the metadata are converted into a
#' SingleCellExperiment object using the CATALYST R/Bioconductor package.
#' 2. Clustering: We apply Louvain algorithm using the R package
#' igraph to cluster the expression values by the type markers
#' (surface markers).
#' 3. Median: Medians are calculated within a cluster for every
#' signaling marker and subject.
#' 4. Aggregating and converting the data: We convert the
#' aggregated data into a SummarizedExperiment.
#' The row meta-data indicates
#' "cluster" corresponding to the cluster id for each protein marker.
#' The colData represents the "sample_id", "condition", "patient_id",
#' "ids"
#' The remaining columns indicate median expression intensities
#' for each of the 126 (14 markers * 9 clusters) cluster combination
#' for each sample. 
#' 
#' The HDCytoData package is an extensible resource containing
#' a set of publicly available high-dimensional flow cytometry
#' and mass cytometry (CyTOF) benchmark datasets hosted on
#' Bioconductor’s ExperimentHub platform.
#' 
#' @docType data
#' @format SummarizedExperiment assay object containing
#' 126 cluster-marker median expression intenities (features)
#' of 8 subjects (samples).
#'
#' @references
#' Weber, M L, Soneson, Charlotte (2019). 
#' “HDCytoData: Collection of high-dimensional cytometry 
#' benchmark datasets in Bioconductor object formats.” 
#' F1000Research, 8(v2), 1459.
#'
# 'Bodenmiller, B., Zunder, E., Finck, R. et al.
# 'Multiplexed mass cytometry profiling of cellular 
# 'states perturbed by small-molecule regulators. 
# 'Nat Biotechnol 30, 858–867 (2012). 
# 'https://doi.org/10.1038/nbt.2317
#'
#' @keywords datasets
#' @examples
#' data(cytoHDBMW)
#' @usage data(cytoHDBMW)
"cytoHDBMW"