diff --git a/src/v3/HTRsim/R/countsGenerator.R b/src/v3/HTRsim/R/countsGenerator.R
index a44e31e9e098a4c26a3adf9a5397a02bae57d734..6f723f6fe73756ffe798511228f5d2cbc7c44641 100644
--- a/src/v3/HTRsim/R/countsGenerator.R
+++ b/src/v3/HTRsim/R/countsGenerator.R
@@ -215,6 +215,7 @@ uniform_replication <- function(maxN, n_samples) {
#'
#' @param maxN a integer : number of replicates
#' @param n_samples an integer : number of samples
+#' @import purrr
#' @return a matrix of 0 and 1
#' @export
#'
diff --git a/src/v3/HTRsim/R/loadEmbeddedFiles.R b/src/v3/HTRsim/R/loadEmbeddedFiles.R
new file mode 100644
index 0000000000000000000000000000000000000000..2ba458dcfc33bfda49c3fa9c2bbe57e13f01d224
--- /dev/null
+++ b/src/v3/HTRsim/R/loadEmbeddedFiles.R
@@ -0,0 +1,50 @@
+#' Load beta dtf embedded in package
+#'
+#' @return an object dds.Extraction
+#' @export
+#'
+#' @examples
+loadObservedValues <- function(){
+ ## Import public beta observed
+ fn = system.file("extdata/", "SRP217588_YM_observedParams.rds", package = "HTRsim")
+ dds.extraction = readRDS(file = fn)
+ return(dds.extraction)
+}
+
+#' Load public counts table
+#'
+#' @import dplyr
+#' @import utils
+#' @return dataframe
+#' @export
+#'
+#' @examples
+loadPubliCounTable <- function(){
+ ## Import public counts table
+ fn = system.file("extdata/", "SRP217588_YM_vkallisto.tsv", package = "HTRsim")
+ tabl_cnts <- utils::read.table(file = fn, header = TRUE)
+ rownames(tabl_cnts) <- tabl_cnts$gene_id
+ tabl_cnts <- tabl_cnts %>% dplyr::select(-gene_id) ##suppr colonne GeneID
+ tabl_cnts = tabl_cnts[ order(tabl_cnts %>% rownames()), ]
+ tabl_cnts = tabl_cnts %>% dplyr::select(., !matches( "ru_rm_5"))
+ return(tabl_cnts)
+}
+
+#' Load public design
+#'
+#' @import dplyr
+#' @import utils
+#' @return dataframe
+#' @export
+#'
+#' @examples
+loadPublicDesign <- function(){
+ ## DESIGN
+ fn = system.file("extdata/", "SRP217588_YM_bioDesign.csv", package = "HTRsim")
+ bioDesign <- utils::read.table(file = fn, header = T, sep = ';')
+ ## defining reference
+ bioDesign$genotype <- factor(x = bioDesign$genotype,levels = c("GSY147", "RM11"))
+ bioDesign$environment <- factor(x = bioDesign$environment, levels = c( "untreated", "treated"))
+ bioDesign = bioDesign %>% dplyr::filter(!str_detect(sample, "ru_rm_5") )
+ return(bioDesign)
+}
\ No newline at end of file
diff --git a/src/v3/HTRsim/R/manipulationsDDS_obj.R b/src/v3/HTRsim/R/manipulationsDDS_obj.R
index d36fa152e0839ce71ce0bccb81557460949b53ce..3689f0faf83611321a477df722fe406c32e65d79 100644
--- a/src/v3/HTRsim/R/manipulationsDDS_obj.R
+++ b/src/v3/HTRsim/R/manipulationsDDS_obj.R
@@ -42,12 +42,7 @@ ddsExtraction <- function(dds_obj){
return(list(beta = beta.dtf,
- gene_dispersion = gene_disp,
- beta0.mean = mean(beta.dtf$beta0, na.rm = T), beta0.sd = sd(beta.dtf$beta0, na.rm = T) ,
- betaG.mean = mean(beta.dtf$betaG, na.rm = T), betaG.sd = sd(beta.dtf$betaG, na.rm = T) ,
- betaE.mean = mean(beta.dtf$betaE, na.rm = T) , betaE.sd = sd(beta.dtf$betaE, na.rm = T) ,
- betaGE.mean = mean(beta.dtf$betaGE, na.rm = T) , betaGE.sd = sd(beta.dtf$betaGE, na.rm = T),
- gene_disp.mean = mean(gene_disp, na.rm = T) , gene_disp.sd = sd(gene_disp, na.rm = T)))
+ gene_dispersion = gene_disp))
}
@@ -60,25 +55,10 @@ ddsExtraction <- function(dds_obj){
#'
#' @examples
publicDDS_extraction <- function(){
- ## Import & reshape public counts table
- fn = system.file("extdata/", "SRP217588_YM_vkallisto.tsv", package = "HTRsim")
- tabl_cnts <- utils::read.table(file = fn, header = TRUE)
- rownames(tabl_cnts) <- tabl_cnts$gene_id
- tabl_cnts <- tabl_cnts %>% dplyr::select(-gene_id)##suppr colonne GeneID
- tabl_cnts = tabl_cnts[ order(tabl_cnts %>% rownames()), ]
- ## DESIGN
- fn = system.file("extdata/", "SRP217588_YM_bioDesign.csv", package = "HTRsim")
- bioDesign <- utils::read.table(file = fn, header = T, sep = ';')
-
- ## defining reference
- bioDesign$genotype <- factor(x = bioDesign$genotype,levels = c("GSY147", "RM11"))
- bioDesign$environment <- factor(x = bioDesign$environment, levels = c( "untreated", "treated"))
- bioDesign = bioDesign %>% dplyr::filter(!str_detect(sample, "ru_rm_5") )
- tabl_cnts = tabl_cnts %>% dplyr::select(., !matches( "ru_rm_5"))
-
+ tabl_cnts = loadPubliCounTable()
+ bioDesgin = loadPublicDesign()
## Launch DESEQ2
dds = run.deseq(tabl_cnts, bioDesign = bioDesign)
-
## Extract
dds.extraction = ddsExtraction(dds_obj = dds)
diff --git a/src/v3/HTRsim/R/workflow.R b/src/v3/HTRsim/R/workflow.R
index 41f52db0dca30024f6cba4bc099a4ab60e60f8f7..d09d2e0ab3002f03e15ad69022764916a50a9695 100644
--- a/src/v3/HTRsim/R/workflow.R
+++ b/src/v3/HTRsim/R/workflow.R
@@ -4,21 +4,24 @@
#' @param n_genes number of genes
#' @param n_genotypes number of genotypes
#' @param n_environments number of env
-#' @param fit.mvnorm output of Rfast::mvnorm.mle
+#' @param dds.extraction output of dds.extraction
#' @param max_n_replicates max number of replicates
#' @param uniformNumberOfReplicates boolean
#' @param uniformDispersion boolean
-#' @return counts table
+#' @return list
#' @export
#'
#' @examples
-counTableBuilder <- function(fit.mvnorm = getPublicMvnormFit(),
- n_genes,
- n_genotypes,
- n_environments = 2,
- max_n_replicates,
- uniformNumberOfReplicates = T,
- uniformDispersion = T ) {
+rnaMock <- function(n_genes,
+ n_genotypes,
+ n_environments = 2,
+ max_n_replicates,
+ uniformNumberOfReplicates = T,
+ uniformDispersion = T,
+ dds.extraction = loadObservedValues() ) {
+
+ ## Fit mvnorm ##
+ fit.mvnorm = mvnormFitting(dds.extraction$beta)
##### Ground truth ######
beta.actual = getBetaforSimulation( n_genes,
@@ -48,7 +51,8 @@ counTableBuilder <- function(fit.mvnorm = getPublicMvnormFit(),
sample_id_list = sample_ids,
replication.matx = designReplication.matx)
- return( countTable )
+ return( list( countTable = countTable, dispersion = dispersion.matrix,
+ beta = beta.actual, mvnorm = fit.mvnorm ))
}