From 6b964918fd9572d6f1b17d2324c92a2df735c147 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 20 Apr 2018 11:34:27 -0500
Subject: [PATCH] Load 'methods' package at the start of every R script as
 Rscript no longer auto loads it

---
 r.scripts/sc_CI.TestData.Create.R     | 1 +
 r.scripts/sc_Cluster.R                | 1 +
 r.scripts/sc_D-SampleReorder.R        | 1 +
 r.scripts/sc_DEG.R                    | 1 +
 r.scripts/sc_Demultiplex.R            | 1 +
 r.scripts/sc_LineageSubClust.R        | 1 +
 r.scripts/sc_MergeSubClust.R          | 1 +
 r.scripts/sc_PC.Score.NE.R            | 1 +
 r.scripts/sc_PC.Score.Stress.R        | 1 +
 r.scripts/sc_QC.R                     | 1 +
 r.scripts/sc_QuSAGE.Lineage.R         | 1 +
 r.scripts/sc_QuSAGE_EpiSubClust.R     | 1 +
 r.scripts/sc_QuSAGE_StSubClust.R      | 1 +
 r.scripts/sc_Seurat.Score.CellCycle.R | 1 +
 r.scripts/sc_Tables.R                 | 1 +
 r.scripts/sc_mkGSEA.R                 | 1 +
 16 files changed, 16 insertions(+)

diff --git a/r.scripts/sc_CI.TestData.Create.R b/r.scripts/sc_CI.TestData.Create.R
index ed87998..280b1bd 100644
--- a/r.scripts/sc_CI.TestData.Create.R
+++ b/r.scripts/sc_CI.TestData.Create.R
@@ -1,5 +1,6 @@
 gc()
 .libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
+library(methods)
 library(readr)
 library(Matrix)
 library(Seurat)
diff --git a/r.scripts/sc_Cluster.R b/r.scripts/sc_Cluster.R
index 1b4e0ec..8daf4e6 100755
--- a/r.scripts/sc_Cluster.R
+++ b/r.scripts/sc_Cluster.R
@@ -1,5 +1,6 @@
 gc()
 .libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
+library(methods)
 library(optparse)
 library(Seurat)
 library(readr)
diff --git a/r.scripts/sc_D-SampleReorder.R b/r.scripts/sc_D-SampleReorder.R
index bbc6850..d731b7e 100755
--- a/r.scripts/sc_D-SampleReorder.R
+++ b/r.scripts/sc_D-SampleReorder.R
@@ -1,5 +1,6 @@
 gc()
 .libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
+library(methods)
 library(optparse)
 library(Seurat)
 
diff --git a/r.scripts/sc_DEG.R b/r.scripts/sc_DEG.R
index 7e67625..983329f 100755
--- a/r.scripts/sc_DEG.R
+++ b/r.scripts/sc_DEG.R
@@ -1,5 +1,6 @@
 gc()
 .libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
+library(methods)
 library(optparse)
 library(Seurat)
 
diff --git a/r.scripts/sc_Demultiplex.R b/r.scripts/sc_Demultiplex.R
index 446c7fd..3906f98 100755
--- a/r.scripts/sc_Demultiplex.R
+++ b/r.scripts/sc_Demultiplex.R
@@ -1,5 +1,6 @@
 gc()
 .libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
+library(methods)
 library(optparse)
 library(Seurat)
 library(readr)
diff --git a/r.scripts/sc_LineageSubClust.R b/r.scripts/sc_LineageSubClust.R
index 3ab2995..f579955 100755
--- a/r.scripts/sc_LineageSubClust.R
+++ b/r.scripts/sc_LineageSubClust.R
@@ -1,5 +1,6 @@
 gc()
 .libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
+library(methods)
 library(optparse)
 library(Seurat)
 
diff --git a/r.scripts/sc_MergeSubClust.R b/r.scripts/sc_MergeSubClust.R
index 1b1ed90..604ed0f 100755
--- a/r.scripts/sc_MergeSubClust.R
+++ b/r.scripts/sc_MergeSubClust.R
@@ -1,5 +1,6 @@
 gc()
 .libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
+library(methods)
 library(optparse)
 library(Seurat)
 
diff --git a/r.scripts/sc_PC.Score.NE.R b/r.scripts/sc_PC.Score.NE.R
index 9b95a2f..6f85de2 100755
--- a/r.scripts/sc_PC.Score.NE.R
+++ b/r.scripts/sc_PC.Score.NE.R
@@ -1,5 +1,6 @@
 gc()
 .libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
+library(methods)
 library(optparse)
 library(Seurat)
 library(readr)
diff --git a/r.scripts/sc_PC.Score.Stress.R b/r.scripts/sc_PC.Score.Stress.R
index e6661c4..4a17509 100755
--- a/r.scripts/sc_PC.Score.Stress.R
+++ b/r.scripts/sc_PC.Score.Stress.R
@@ -1,5 +1,6 @@
 gc()
 .libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
+library(methods)
 library(optparse)
 library(Seurat)
 library(readr)
diff --git a/r.scripts/sc_QC.R b/r.scripts/sc_QC.R
index 8bfce29..74c811e 100755
--- a/r.scripts/sc_QC.R
+++ b/r.scripts/sc_QC.R
@@ -1,5 +1,6 @@
 gc()
 .libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
+library(methods)
 library(optparse)
 library(Seurat)
 library(readr)
diff --git a/r.scripts/sc_QuSAGE.Lineage.R b/r.scripts/sc_QuSAGE.Lineage.R
index d017fee..9c28794 100755
--- a/r.scripts/sc_QuSAGE.Lineage.R
+++ b/r.scripts/sc_QuSAGE.Lineage.R
@@ -1,5 +1,6 @@
 gc()
 .libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
+library(methods)
 library(optparse)
 library(Seurat)
 library(readr)
diff --git a/r.scripts/sc_QuSAGE_EpiSubClust.R b/r.scripts/sc_QuSAGE_EpiSubClust.R
index 0d93b77..91fd7ef 100755
--- a/r.scripts/sc_QuSAGE_EpiSubClust.R
+++ b/r.scripts/sc_QuSAGE_EpiSubClust.R
@@ -1,5 +1,6 @@
 gc()
 .libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
+library(methods)
 library(optparse)
 library(Seurat)
 library(readr)
diff --git a/r.scripts/sc_QuSAGE_StSubClust.R b/r.scripts/sc_QuSAGE_StSubClust.R
index ac51bce..586f2bf 100755
--- a/r.scripts/sc_QuSAGE_StSubClust.R
+++ b/r.scripts/sc_QuSAGE_StSubClust.R
@@ -1,5 +1,6 @@
 gc()
 .libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
+library(methods)
 library(optparse)
 library(Seurat)
 library(readr)
diff --git a/r.scripts/sc_Seurat.Score.CellCycle.R b/r.scripts/sc_Seurat.Score.CellCycle.R
index f3126ee..a531ec7 100755
--- a/r.scripts/sc_Seurat.Score.CellCycle.R
+++ b/r.scripts/sc_Seurat.Score.CellCycle.R
@@ -1,5 +1,6 @@
 gc()
 .libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
+library(methods)
 library(optparse)
 library(Seurat)
 library(readr)
diff --git a/r.scripts/sc_Tables.R b/r.scripts/sc_Tables.R
index 89f81ed..d306ba1 100755
--- a/r.scripts/sc_Tables.R
+++ b/r.scripts/sc_Tables.R
@@ -1,5 +1,6 @@
 gc()
 .libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
+library(methods)
 library(optparse)
 library(Seurat)
 
diff --git a/r.scripts/sc_mkGSEA.R b/r.scripts/sc_mkGSEA.R
index 6952e4e..3497a3b 100755
--- a/r.scripts/sc_mkGSEA.R
+++ b/r.scripts/sc_mkGSEA.R
@@ -1,4 +1,5 @@
 .libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
+library(methods)
 library(optparse)
 library(Seurat)
 library(readr)
-- 
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