% Generated by roxygen2: do not edit by hand % Please edit documentation in R/abundance.R \name{diffAbundanceFET} \alias{diffAbundanceFET} \title{Calculate Differential Abundance with FET} \usage{ diffAbundanceFET(inSCE, cluster, variable, control, case, analysisName) } \arguments{ \item{inSCE}{A \code{\link[SingleCellExperiment]{SingleCellExperiment}} object.} \item{cluster}{A single \code{character}, specifying the name to store the cluster label in \code{\link{colData}}.} \item{variable}{A single \code{character}, specifying the name to store the phenotype labels in \code{\link{colData}}.} \item{control}{\code{character}. Specifying one or more categories that can be found in the vector specified by \code{variable}.} \item{case}{\code{character}. Specifying one or more categories that can be found in the vector specified by \code{variable}.} \item{analysisName}{A single \code{character}. Will be used for naming the result table, which will be saved in metadata slot.} } \value{ The original \code{\link[SingleCellExperiment]{SingleCellExperiment}} object with \code{metadata(inSCE)} updated with a list \code{diffAbundanceFET}, containing a new \code{data.frame} for the analysis result, named by \code{analysisName}. The \code{data.frame} contains columns for number and fraction of cells that belong to different cases, as well as "Odds_Ratio", "PValue" and "FDR". } \description{ Calculate Differential Abundance with FET } \details{ This function will calculate the cell counting and fraction by dividing all cells to groups specified by the arguments, together with statistical summary by performing Fisher Exact Tests (FET). } \examples{ data("mouseBrainSubsetSCE", package = "singleCellTK") mouseBrainSubsetSCE <- diffAbundanceFET(inSCE = mouseBrainSubsetSCE, cluster = "tissue", variable = "level1class", case = "oligodendrocytes", control = "microglia", analysisName = "diffAbundFET") }