From 9725b09580a74e7342e1b582cbbedb0e547f6dbc Mon Sep 17 00:00:00 2001
From: almeidasilvaf <fabricio_almeidasilva@hotmail.com>
Date: Fri, 17 Nov 2023 15:17:40 +0100
Subject: [PATCH] Added option to specify level for midparent values

---
 R/02_de_analyses.R  | 8 ++++++--
 man/get_deg_list.Rd | 5 +++++
 2 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/R/02_de_analyses.R b/R/02_de_analyses.R
index 86f0b1d..c9ed39f 100644
--- a/R/02_de_analyses.R
+++ b/R/02_de_analyses.R
@@ -13,6 +13,9 @@
 #' @param offspring Character indicating which level of the 
 #' variable \strong{coldata_column} represents the offspring (hybrid
 #' or allopolyploid). Default: "F1"
+#' @param midparent Character indicating which level of the variable
+#' \strong{coldata_column} represents the midparent value. Default:
+#' "midparent", as returned by \code{add_midparent_expression()}.
 #' @param spikein_norm Logical indicating whether or not to normalize data
 #' using spike-ins. Default: FALSE.
 #' @param spikein_pattern Character with the pattern (regex) to use
@@ -55,7 +58,8 @@
 #' deg_list <- get_deg_list(se, spikein_norm = TRUE)
 get_deg_list <- function(
         se, coldata_column = "Generation", 
-        parent1 = "P1", parent2 = "P2", offspring = "F1",
+        parent1 = "P1", parent2 = "P2", offspring = "F1", 
+        midparent = "midparent",
         spikein_norm = FALSE, spikein_pattern = "ERCC",
         lfcThreshold = 0,
         alpha = 0.01,
@@ -88,7 +92,7 @@ get_deg_list <- function(
         "P2_vs_P1" = c(parent2, parent1),
         "F1_vs_P1" = c(offspring, parent1),
         "F1_vs_P2" = c(offspring, parent2),
-        "F1_vs_midparent" = c(offspring, "midparent")
+        "F1_vs_midparent" = c(offspring, midparent)
     )
     
     dge_list <- lapply(contrasts, function(x) {
diff --git a/man/get_deg_list.Rd b/man/get_deg_list.Rd
index 43922b9..db08be7 100644
--- a/man/get_deg_list.Rd
+++ b/man/get_deg_list.Rd
@@ -10,6 +10,7 @@ get_deg_list(
   parent1 = "P1",
   parent2 = "P2",
   offspring = "F1",
+  midparent = "midparent",
   spikein_norm = FALSE,
   spikein_pattern = "ERCC",
   lfcThreshold = 0,
@@ -35,6 +36,10 @@ variable \strong{coldata_column} represents parent 2. Default: "P2".}
 variable \strong{coldata_column} represents the offspring (hybrid
 or allopolyploid). Default: "F1"}
 
+\item{midparent}{Character indicating which level of the variable
+\strong{coldata_column} represents the midparent value. Default:
+"midparent", as returned by \code{add_midparent_expression()}.}
+
 \item{spikein_norm}{Logical indicating whether or not to normalize data
 using spike-ins. Default: FALSE.}