diff --git a/src/htrsim/main.R b/src/htrsim/main.R index 505fe7594e4f2bc773f7496c84ce136d96d9f580..073ec92c7368d29ae31cd5cff45ab178bd47a7f2 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 40526a2974557ab05b80cbb0130860481dd2d3d4..1c201fe629d7a1c93cea80638405d4c0366afff8 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) + ```