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Commit 6328af1f authored by Arnaud Duvermy's avatar Arnaud Duvermy
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update

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######################### 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
......
......@@ -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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