From fb9993537c756206e9a130a91d9b09a8d3479424 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?= <antoniop.camargo@gmail.com>
Date: Tue, 26 Jun 2018 16:53:24 -0300
Subject: [PATCH] Add gene-level 'obs_raw' support to 'sleuth_to_matrix'

---
 R/matrix.R | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/R/matrix.R b/R/matrix.R
index 4ffecf3..ab3d63d 100644
--- a/R/matrix.R
+++ b/R/matrix.R
@@ -40,12 +40,6 @@ sleuth_to_matrix <- function(obj, which_df, which_units) {
 
   which_units <- check_quant_mode(obj, which_units)
 
-  if (obj$gene_mode && which_df == "obs_raw") {
-    warning("This object is in gene mode, and the raw values are ",
-            "transcripts. Using 'obs_norm' instead.")
-    which_df <- "obs_norm"
-  }
-
   data <- as.data.frame(obj[[which_df]])
 
   res <- list()
@@ -56,5 +50,13 @@ sleuth_to_matrix <- function(obj, which_df, which_units) {
   s_data$target_id <- NULL
   s_data <- as.matrix(s_data)
 
+  if (obj$gene_mode && which_df == "obs_raw") {
+    if (which_units == "scaled_reads_per_base") {
+      s_data <- t(t(s_data)*obj$est_counts_sf)
+    } else {
+      s_data <- t(t(s_data)*obj$tpm_sf)
+    }
+  }
+
   s_data
 }