diff --git a/R/testSlope.R b/R/testSlope.R index 16612ff..eefe804 100644 --- a/R/testSlope.R +++ b/R/testSlope.R @@ -8,7 +8,7 @@ #' @importFrom dplyr arrange desc mutate if_else with_groups #' @importFrom stats p.adjust #' @param test.dyn.res The list returned by \code{\link{testDynamic}} - no extra processing required. Defaults to NULL. -#' @param p.adj.method The method used to adjust the \emph{p}-values for each coefficient. Defaults to "holm". +#' @param p.adj.method The method used to adjust the \emph{p}-values for each coefficient. Defaults to "fdr". #' @param fdr.cutoff The FDR threshold for determining statistical significance. Defaults to 0.01. #' @return A dataframe containing the genes, breakpoints, and coefficient \emph{p}-values from each model. #' @seealso \code{\link{testDynamic}} @@ -19,7 +19,7 @@ #' slope_test_res <- testSlope(scLANE_models) testSlope <- function(test.dyn.res = NULL, - p.adj.method = "holm", + p.adj.method = "fdr", fdr.cutoff = 0.01) { # check inputs if (is.null(test.dyn.res)) { stop("You forgot to provide results from testDynamic() to testSlope().") } diff --git a/man/testSlope.Rd b/man/testSlope.Rd index 755ea44..c45075e 100644 --- a/man/testSlope.Rd +++ b/man/testSlope.Rd @@ -4,12 +4,12 @@ \alias{testSlope} \title{Test whether a gene is dynamic over a pseudotime interval.} \usage{ -testSlope(test.dyn.res = NULL, p.adj.method = "holm", fdr.cutoff = 0.01) +testSlope(test.dyn.res = NULL, p.adj.method = "fdr", fdr.cutoff = 0.01) } \arguments{ \item{test.dyn.res}{The list returned by \code{\link{testDynamic}} - no extra processing required. Defaults to NULL.} -\item{p.adj.method}{The method used to adjust the \emph{p}-values for each coefficient. Defaults to "holm".} +\item{p.adj.method}{The method used to adjust the \emph{p}-values for each coefficient. Defaults to "fdr".} \item{fdr.cutoff}{The FDR threshold for determining statistical significance. Defaults to 0.01.} }