added summary.scLANE() function -- closes #151

NAMESPACE

@@ -1,5 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(print,summary.scLANE)
+S3method(summary,scLANE)
 export(bootstrapRandomEffects)
 export(chooseCandidateGenes)
 export(clusterGenes)

R/summary.R

@@ -0,0 +1,55 @@
+#' Summary method for scLANE objects. 
+#' 
+#' @name summary.scLANE
+#' @author Jack R. Leary
+#' @importFrom purrr map reduce 
+#' @importFrom stats p.adjust 
+#' @param test.dyn.res The nested list returned by \code{\link{testDynamic}}. Defaults to NULL. 
+#' @param (Optional) The method used to adjust \emph{p}-values for multiple hypothesis testing. Defaults to "fdr".
+#' @param fdr.cutoff (Optional) The FDR threshold for determining statistical significance. Defaults to 0.01.
+#' @return A summary list with aggregated statistics concerning the trajectory DE tests from \code{scLANE}. 
+#' @export
+#' @examples
+#' data(scLANE_models)
+#' summary(scLANE_models)
+
+summary.scLANE <- function(test.dyn.res = NULL, 
+                           p.adj.method = "fdr", 
+                           fdr.cutoff = 0.01) {
+  if (!inherits(test.dyn.res, "scLANE")) { stop("The input must be an object of class 'scLANE'.") }
+  summary_stats <- list()
+  summary_stats$n_lineages <- length(test.dyn.res[[1]])
+  summary_stats$n_genes <- length(test.dyn.res)
+  p_values <- purrr::map(test.dyn.res, \(g) {
+    purrr::map(g, \(l) {
+      l$P_Val
+    })
+  })
+  p_values <- purrr::reduce(purrr::reduce(p_values, c), c)
+  adj_p_values <- stats::p.adjust(sort(p_values), method = p.adj.method)
+  summary_stats$n_significant_genes <- sum(adj_p_values < fdr.cutoff, na.rm = TRUE)
+  summary_stats$mean_adj_p_value <- mean(adj_p_values, na.rm = TRUE)
+  summary_stats$test_type <- ifelse(test.dyn.res[[1]][[1]]$Test_Stat_Type == "LRT", 
+                                    "Likelihood Ratio Test", 
+                                    "Wald Test")
+  class(summary_stats) <- "summary.scLANE"
+  return(summary_stats)
+}
+
+#' Print method for summary.scLANE objects. 
+#' 
+#' @name print.summary.scLANE
+#' @author Jack R. Leary
+#' @param x An object of class summary.scLANE. 
+#' @export
+
+print.summary.scLANE <- function(x) {
+  cat("Summary of scLANE Model Results\n")
+  cat("-------------------------------\n")
+  cat("Test used: ", x$test_type, "\n")
+  cat("Total genes analyzed: ", x$n_genes, "\n")
+  cat("Total lineages analyzed: ", x$n_lineages, "\n")
+  cat("Mean adjusted p-value: ", format(x$mean_adj_p_value, digits = 5), "\n")
+  cat("Number of significant gene-lineage tests: ", x$n_significant_genes, "\n")
+  invisible(x)
+}