update

src/htrsim/main.R

-######################### 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

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)
+
 ```