diff --git a/README.md b/README.md index 6bb9ed228341a2216d1cd3516c6cfa907ad4762c..1fad2f658b3f5b33f2f08c3dfc26b59419c5153d 100644 --- a/README.md +++ b/README.md @@ -86,18 +86,35 @@ In the realm of RNAseq analysis, various key experimental parameters play a cruc ## Getting started + +### Init a design and simulate RNAseq data + ``` library('HTRfit') ## -- init a design -input_var_list <- init_variable( name = "varA", mu = 0, sd = 0.29, level = 60) %>% +input_var_list <- init_variable( name = "varA", mu = 0, sd = 0.29, level = 2000) %>% init_variable( name = "varB", mu = 0.27, sd = 0.6, level = 2) %>% add_interaction( between_var = c("varA", "varB"), mu = 0.44, sd = 0.89) ## -- simulate RNAseq data mock_data <- mock_rnaseq(input_var_list, - n_genes = 30, - min_replicates = 10, - max_replicates = 10, - basal_expression = 5 ) + n_genes = 30000, + min_replicates = 4, + max_replicates = 4 ) +``` + + +The simulation process in HTRfit has been optimized to generate RNAseq counts for 30,000 genes and 4,000 experimental conditions, each replicated 4 times, resulting in a total of 16,000 samples, in less than 5 minutes. However, the object generated by the framework under these conditions can consume a significant amount of RAM, approximately 50 GB. For an equivalent simulation with 6,000 genes, less than a minute and 10 GB of RAM are required. + + +<div id="bg" align="center"> + <img src="./vignettes/figs/simulation_step.png" width="500" height="300"> +</div> + + + +### Fit your model + +``` ## -- prepare data & fit a model with mixed effect data2fit = prepareData2fit(countMatrix = mock_data$counts, metadata = mock_data$metadata, @@ -106,8 +123,12 @@ l_tmb <- fitModelParallel(formula = kij ~ varB + (varB | varA), data = data2fit, group_by = "geneID", family = glmmTMB::nbinom2(link = "log"), - log_file = "log.txt", n.cores = 1) +``` + +### Evalutation + +``` ## -- evaluation resSimu <- simulationReport(mock_data, list_tmb = l_tmb, diff --git a/vignettes/figs/simulation_step.png b/vignettes/figs/simulation_step.png new file mode 100644 index 0000000000000000000000000000000000000000..3ad52b7527046b369f00738f3e9438ac913fc469 Binary files /dev/null and b/vignettes/figs/simulation_step.png differ