README.md

In angy89/TinderMIX: TinderMIX: An R package to cluster gene expression by contour plots

TinderMIX

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.

Example of R Usage

```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)

plot heatmap with number of genes for each label

source("R/plotting_functions.R")

gene_plot = TinderMIX::plot_number_genes_labels(res = DDRGene,drugName = drugName,timeLabels = timeLabels,doseLabels = doseLabels) plot(gene_plot)

plot radial plots with number of genes for the 12 combination of dose and time points

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") ```

angy89/TinderMIX documentation built on Nov. 26, 2020, 9:26 p.m.