Add log fold-change

code/method-pars.R

@@ -73,11 +73,11 @@ random_pars <- expand_grid(
 ) %>%
   mutate(file_name = paste0(method))
 
-difference_pars <- expand_grid(
-  method = "difference",
-  summary = c("log_fc")
+logfc_pars <- expand_grid(
+  method = "logfc",
+  rankby = c("abs", "raw")
 ) %>%
-  mutate(file_name = paste0(method, "_", summary))
+  mutate(file_name = paste0(method, "_", rankby))
 
 glmgampoi_pars <- expand_grid(
   method = "glmgampoi",
@@ -109,7 +109,7 @@ method_pars_data <- list(
   presto_pars,
   rankcorr_pars,
   random_pars,
-  difference_pars,
+  logfc_pars,
   glmgampoi_pars,
   #smash_pars,
   nsforest_pars,

code/run-difference.R → code/run-logfc.R

@@ -6,11 +6,9 @@
 #' @return A list containing the time of the computation and results of the
 #'  method.
 #'
-run_difference <- function(sce, pars) {
+run_logfc <- function(sce, pars) {
 
-  if (pars$summary != "log_fc") {
-    stop("Invalid summary parameter", call. = FALSE)
-  }
+  stopifnot(pars$rankby %in% c("raw", "abs"))
 
   times <- system.time({
 
@@ -39,7 +37,13 @@ run_difference <- function(sce, pars) {
         gene = rownames(sce),
         cluster = group
       )
-      group_df <- dplyr::arrange(group_df, desc(abs(log_fc)))
+
+      if (pars$rankby == "abs") {
+        group_df <- dplyr::arrange(group_df, desc(abs(log_fc)))
+      } else if (pars$rankby == "raw") {
+        group_df <- dplyr::arrange(group_df, desc(log_fc))
+      }
+
       out[[i]] <- group_df
     }