Man pages for anschue/toxprofileR
Functions for Retrieving Dynamic Toxicogenomic Fingerprints
| arrayqc | Array Quality Control |
| calc_logfc | Calculate logFC |
| calc_logfc_public | Calculate logFC of public microarray data |
| create_nodelist | Create logFC Nodelist |
| create_shiny_nodeplotlist | Create nodeplot list for shiny app |
| create_shiny_plotlist | Create Shiny Plotlist |
| create_tox_universe | Create toxicogenomic universe |
| elist.median | Calculate Probe Medians of ExpressionSet |
| enrich_clusters | Functional enrichment of universe clusters |
| fit_apical | Fit Apical |
| fit_tcta | Fit regression model on toxicogenomic profile |
| gauss_gauss | Gauss-Gauss Model |
| getBM_annotation | get biomaRt annotaiton |
| get_CI_diffs | Get Difference of Confidence Interval |
| get_extrema_nodes | Get extreme values across several experiments per toxnode |
| get_hits_exons | Get Exon Hits |
| get_hits_genome | Get Genome hits |
| get_sig_level | Get significance level |
| get_tcta_params | Get regression model parameters for one node |
| hill_gauss | Hill-Gauss Model |
| importData | Import Array Data |
| nodelist_from_logFC | Create nodelist from logFC dataframe |
| normalizeBatch | Normalize Batch |
| plot3D_node | Plot noderesponse as surface |
| plot_nodecode | Plot Nodecode |
| plot_noderesponse | Plot noderesponse |
| plot_noderesponse_time | Plot noderesponse for selected timepoint |
| plot_portrait | Plot Tox Portrait |
| plot_portrait_grid | Plot portrait grid |
| preprocess | Preprocess Data |
| qc_plots | QC plots |
| read_raw_public | Read Microarray data from GEO or ArrayExpress |
| remove_outliers | Remove outliers |
| save_shiny_data | Save Shiny Data |
| sens_t | Sensitivity function |
| spline_fit | Fit 3-D spline to time and concentration dependent data |
| tfp_browser | Run fingerprint browser |
