TinderMIX is a new computational framework for dose- and time- dependent gene expression analysis which aims to identify groups of genes that show a dynamic dose-response behaviour.
```R library(TinderMIX)
pheno = read.delim("sample_data/WY-14643_pheno.txt") exp_data = read.delim("sample_data/WY-14643_exp.txt") drugName = "WY-14643" fc_data = TinderMIX::compute_fc(exp_data = exp_data,pheno_data = pheno,dose_index = 2,time_index = 4)
responsive_genes = rownames(fc_data$fc_data)[1:100] exp_data = fc_data$fc_data pheno_data = fc_data$pdata
source("sample_data/set_parameters.R")
contour_res = suppressMessages(TinderMIX::create_contour(exp_data, pheno_data, responsive_genes, dose_index = dose_index, time_point_index = time_point_index , gridSize = gridSize, pvalFitting = pvalFitting, pvalFitting.adj.method = pvalFitting.adj.method, logScale = T, modelSelection = 1:3))
print("Step 4: Run BMD_IC50 analysis on every gene") DDRGene = TinderMIX::run_all_BMD_IC50(contour_res = contour_res, activity_threshold = activity_threshold, BMD_response_threshold = BMD_response_threshold, mode=mode, nDoseInt=nDoseInt, nTimeInt=nTimeInt, doseLabels = doseLabels, timeLabels = timeLabels, tosave=FALSE, addLegend = FALSE, path = ".", relGenes = contour_res$ggenes, toPlot = FALSE)
plot_dynamic_dose_responsive_map(contour_res, geneName="Gad1",activity_threshold, BMD_response_threshold,mode,nTimeInt,nDoseInt, timeLabels,doseLabels)
gene_plot = TinderMIX::plot_number_genes_labels(res = DDRGene,drugName = drugName,timeLabels = timeLabels,doseLabels = doseLabels) plot(gene_plot)
label_plot = TinderMIX::plot_cake_diagrams_time_dose_effect(res = DDRGene, timeLabels = timeLabels,doseLabels = doseLabels)
res = TinderMIX::create_gene_table(DDRGene,contour_res, nTimeInt,nDoseInt,biomart_dataset = "rnorvegicus_gene_ensembl") ```
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