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@@ -16,14 +16,14 @@
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#' \code{resultNamePrefix_CDF}. If this parameter is set to \code{NULL}, then
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#' \code{"VAM_geneSetCollectionName_"} will be used. Default \code{NULL}.
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#' @param center Boolean. If \code{TRUE}, values will be mean centered when
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-#' computing the Mahalanobis statistic. Default \code{TRUE}.
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+#' computing the Mahalanobis statistic. Default \code{FALSE}.
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#' @param gamma Boolean. If \code{TRUE}, a gamma distribution will be fit to
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#' the non-zero squared Mahalanobis distances computed from a row-permuted
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#' version of the gene expression matrix. The estimated gamma distribution will
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#' be used to compute a one-sided p-value for each cell. If \code{FALSE}, the
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#' p-value will be computed using the standard chi-square approximation for the
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#' squared Mahalanobis distance (or non-central if \code{center = FALSE}).
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-#' Default \code{FALSE}.
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+#' Default \code{TRUE}.
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#' @importFrom methods slot
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#' @return A \linkS4class{SingleCellExperiment} object with VAM metrics stored
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#' in \code{reducedDim} as \code{VAM_NameOfTheGeneset_Distance} and
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