R/datasets.R

In lubianat/FCBF: Fast Correlation Based Filter for Feature Selection

#' @importMethodsFrom SummarizedExperiment assay colData
NULL

#' Dengue infected macrophages; gene expression data from GEO study GSE110496
#'
#' Expression data from single cells, from  adengue virus infection study by
#' Zanini et al, #' 2018. The expression was filtered to get cells 12 hours
#' after infection with #' a multiplicity of infection (moi) of 1 (dengue)
#' or uninfected(ctrl). Gene counts were normalized via Bioconductor
#' package "SCNorm".
#'
#' Gene expression has to be discretized for use in FCBF.
#'

#' @name scDengue
#' @docType data
#' @usage data(scDengue)
#' @format An object of class \code{SingleCellExperiment}
#' @keywords datasets, dengue, single-cell
#' @references Zanini, F., Pu, S. Y., Bekerman, E., Einav, S., & Quake, S. R.
#' (2018). Single-cell transcriptional dynamics of flavivirus infection.
#' Elife, 7, e32942.
#' \href{https://www.ncbi.nlm.nih.gov/pubmed/29451494}{PubMed}
#' @source \href{https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110496}{GEO}
#' @examples
#' data(scDengue)
#' exprs <- SummarizedExperiment::assay(scDengue, 'logcounts')
#' infection <- SummarizedExperiment::colData(scDengue)
#' target <- infection$infection
#' # Discretize gene expression
#' discrete_expression <- as.data.frame(discretize_exprs(exprs))
#' fcbf_features <- fcbf(discrete_expression,
#'                               target,
#'                               minimum_su = 0.05,
#'                               verbose = TRUE)
"scDengue"