diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index ed49bb3..90184bd 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -43,8 +43,8 @@ jobs: shell: bash - name: Upload test results - if: failure() + if: always() uses: actions/upload-artifact@v3 with: - name: coverage-test-failures + name: coverage-test-upload path: ${{ runner.temp }}/package diff --git a/R/testDynamic.R b/R/testDynamic.R index e9a8a17..a7e583b 100644 --- a/R/testDynamic.R +++ b/R/testDynamic.R @@ -40,7 +40,7 @@ #' \item If using the GEE or GLMM model architectures, ensure that the observations are sorted by subject ID (this is assumed by the underlying fit implementations). If they are not, the models will error out. #' \item If \code{gee.bias.correction.method} is set to "kc" or "df", a bias adjustment will be used to inflate the robust variance-covariance matrix prior to estimating the Wald test statistic. This is useful when the number of subjects is small and / or the number of per-subject observations is very large. Doing so will remove the bias in the sandwich estimator in small-sample cases. Currently, we suggest keeping this NULL and using the model-based variance estimates and specifying the "ar1" correlation structure. #' } -#' @return A list of lists, where each element is a gene and each gene contains sublists for each element. Each gene-lineage sublist contains a gene name, lineage number, default \code{marge} vs. null model test results, model statistics, and fitted values. Use \code{\link{getResultsDE}} to tidy the results. +#' @return A list of lists, where each element is a gene and each gene contains sublists for each lineage. Each gene-lineage sublist contains a gene name, lineage number, default \code{marge} vs. null model test results, model statistics, and fitted values. Use \code{\link{getResultsDE}} to tidy the results. #' @seealso \code{\link{getResultsDE}} #' @seealso \code{\link{testSlope}} #' @seealso \code{\link{marge2}} 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/testDynamic.Rd b/man/testDynamic.Rd index f067ad4..efc641a 100644 --- a/man/testDynamic.Rd +++ b/man/testDynamic.Rd @@ -54,7 +54,7 @@ testDynamic( \item{random.seed}{(Optional) The random seed used to initialize RNG streams in parallel. Defaults to 312.} } \value{ -A list of lists, where each element is a gene and each gene contains sublists for each element. Each gene-lineage sublist contains a gene name, lineage number, default \code{marge} vs. null model test results, model statistics, and fitted values. Use \code{\link{getResultsDE}} to tidy the results. +A list of lists, where each element is a gene and each gene contains sublists for each lineage. Each gene-lineage sublist contains a gene name, lineage number, default \code{marge} vs. null model test results, model statistics, and fitted values. Use \code{\link{getResultsDE}} to tidy the results. } \description{ This function tests whether a NB \code{marge} model is better than a null (intercept-only) model using the Likelihood Ratio Test. In effect, the test tells us whether a gene's expression changes (in any way) over pseudotime. 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.} }