From f97e650d22dd45286a17dd8acafc341bed7cd1e8 Mon Sep 17 00:00:00 2001
From: aduvermy <arnaud.duvermy@ens-lyon.fr>
Date: Fri, 22 Apr 2022 15:47:25 +0200
Subject: [PATCH] update package
---
src/htrsim/DESCRIPTION | 6 ++++-
src/htrsim/NAMESPACE | 3 +++
src/htrsim/devtools_history.R | 4 +++
src/htrsim/inst/extdata/public_bioDesign.csv | 26 ++++++++++----------
4 files changed, 25 insertions(+), 14 deletions(-)
diff --git a/src/htrsim/DESCRIPTION b/src/htrsim/DESCRIPTION
index 305c99c..a5ca29c 100644
--- a/src/htrsim/DESCRIPTION
+++ b/src/htrsim/DESCRIPTION
@@ -24,4 +24,8 @@ Imports:
data.table,
plyr,
reshape2,
- tidyr
+ tidyr,
+ S4Vectors,
+ readr,
+ testthat
+Config/testthat/edition: 3
diff --git a/src/htrsim/NAMESPACE b/src/htrsim/NAMESPACE
index 5958cec..b6f56d7 100644
--- a/src/htrsim/NAMESPACE
+++ b/src/htrsim/NAMESPACE
@@ -2,6 +2,7 @@
export(estim.alpha)
export(estim.mu)
+export(estim.mu_beta)
export(generate_counts)
export(handle_except)
export(htrsim)
@@ -11,10 +12,12 @@ export(run.deseq)
export(setup_countGener)
import(BiocGenerics)
import(DESeq2)
+import(S4Vectors)
import(data.table)
import(dplyr)
import(plyr)
import(purrr)
+import(readr)
import(reshape2)
import(stats)
import(stringr)
diff --git a/src/htrsim/devtools_history.R b/src/htrsim/devtools_history.R
index 69ccee8..38b57d8 100644
--- a/src/htrsim/devtools_history.R
+++ b/src/htrsim/devtools_history.R
@@ -11,4 +11,8 @@ usethis::use_package("data.table")
usethis::use_package("plyr")
usethis::use_package("reshape2")
usethis::use_package("tidyr")
+usethis::use_package("S4Vectors")
+usethis::use_package("readr")
+usethis::use_package("testthat")
+usethis::use_test("name")
devtools::load_all()
diff --git a/src/htrsim/inst/extdata/public_bioDesign.csv b/src/htrsim/inst/extdata/public_bioDesign.csv
index a4e913c..9c0ad93 100644
--- a/src/htrsim/inst/extdata/public_bioDesign.csv
+++ b/src/htrsim/inst/extdata/public_bioDesign.csv
@@ -1,13 +1,13 @@
-sample;env;mutant;mutant_env
-Msn2D_KCl_rep1;kcl;msn2D;msn2D_kcl
-Msn2D_KCl_rep2;kcl;msn2D;msn2D_kcl
-Msn4D_KCl_rep1;kcl;msn4D;msn4D_kcl
-Msn4D_KCl_rep2;kcl;msn4D;msn4D_kcl
-Msn2D_control_rep1;control;msn2D;msn2D_control
-Msn2D_control_rep1;control;msn2D;msn2D_control
-Msn4D_control_rep1;control;msn4D;msn4D_control
-Msn4D_control_rep2;control;msn4D;msn4D_control
-WT_control_rep1;control;wt;wt_control
-WT_control_rep2;control;wt;wt_control
-WT_KCl_rep1;kcl;wt;wt_kcl
-WT_KCl_rep2;kcl;wt;wt_kcl
+sample;env;genotype
+WT_control_rep1;control;wt
+WT_control_rep2;control;wt
+WT_KCl_rep1;kcl;wt
+WT_KCl_rep2;kcl;wt
+Msn4D_control_rep1;control;msn4D
+Msn4D_control_rep2;control;msn4D
+Msn4D_KCl_rep1;kcl;msn4D
+Msn4D_KCl_rep2;kcl;msn4D
+Msn2D_control_rep1;control;msn2D
+Msn2D_control_rep2;control;msn2D
+Msn2D_KCl_rep1;kcl;msn2D
+Msn2D_KCl_rep2;kcl;msn2D
--
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