From 6328af1f980829fccf75f7e935fe3c9e3b588667 Mon Sep 17 00:00:00 2001
From: aduvermy <arnaud.duvermy@ens-lyon.fr>
Date: Wed, 6 Apr 2022 15:20:54 +0200
Subject: [PATCH] update
---
src/htrsim/main.R | 13 ++++++-------
src/tutorial_htrsim.Rmd | 4 ++--
2 files changed, 8 insertions(+), 9 deletions(-)
diff --git a/src/htrsim/main.R b/src/htrsim/main.R
index 505fe75..073ec92 100644
--- a/src/htrsim/main.R
+++ b/src/htrsim/main.R
@@ -1,22 +1,21 @@
-######################### HTRSIM MAIN SRC ###################################
htrsim <- function(countData, bioDesign, N_replicates){
-
-
+
+
source(file = "/home/rstudio/mydatalocal/counts_simulation/src/htrsim/launch_deseq.R")
dds <- run.deseq(countData, bioDesign)
-
+
source(file="/home/rstudio/mydatalocal/counts_simulation/src/htrsim/input_estimation.R")
mu.input = estim.mu(dds)
alpha.input = estim.alpha(dds)
-
+
source(file="/home/rstudio/mydatalocal/counts_simulation/src/htrsim/setup_cntsGenerator.R")
input = reshape_input2setup(mu.dtf = mu.input, alpha.dtf = alpha.input)
-
+
setup.simulation <- setup_countGener(bioSample_id = input$bioSample_id,
n_rep = N_replicates,
- alpha = input$alpha,
+ alpha = input$alpha,
gene_id = input$gene_id,
mu = input$mu)
## Generate counts
diff --git a/src/tutorial_htrsim.Rmd b/src/tutorial_htrsim.Rmd
index 40526a2..1c201fe 100644
--- a/src/tutorial_htrsim.Rmd
+++ b/src/tutorial_htrsim.Rmd
@@ -64,12 +64,12 @@ tabl_cnts
```{r message=FALSE, warning=FALSE}
## import design of bioProject
-bioDesign <- read_csv2(file = "/home/rstudio/mydatalocal/rna-seq_public_library_investigations/data/design_deseq__PRJNA675209.csv")
+bioDesign <- read.table(file = "/home/rstudio/mydatalocal/rna-seq_public_library_investigations/data/design_deseq__PRJNA675209.csv")
#bioDesign
source(file = "htrsim/main.R")
tabl_cnts %>% dim()
bioDesign %>% dim()
-simul_cnts = htrsim(tabl_cnts, bioDesign = bioDesign, 2)
+
```
--
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