Man pages for marchinilab/SDAtools
SDAtools: A toolkit for SDA
| check_convergence | Check Convergence |
| check_simulation_scores | check_simulation_scores |
| export_data | Export data and labels |
| genome_loadings | Plot Component Loadings by Genomic Location |
| get.location | Load genomic locations from biomart |
| highest_components | Which component has the highest loading for a given gene |
| highest_genes | Which gene has the highest loading for a given component |
| load_chromosome_lengths | Load chromosome lengths |
| load_gene_locations | Load gene coordinates from Ensembl biomart or Cached data |
| loading_distribution | Plot overall distribution of gene loadings |
| load_results | Read SDA output into R list |
| PIP_component_distribution | Plot PIP distribution for a single component |
| PIP_distribution | Plot PIP distribution |
| PIP_threshold_distribution | Plot faction PIP < 0.5 distribution |
| plot_free_energy | Plot free energy over time |
| plot_free_energy_change | Plot change in free energy over time |
| plot_loadings | Plot loadings matrices |
| plot_maximums | Plot maximum score and loading by component |
| plot_PIP | Plot PIP fraction <0.5 by iteration |
| plot_PIP_change | Plot change in fraction of PIPs <0.5 over time |
| plot_scores | Plot Individual Scores |
| plot_scree | Scree Plot |
| random_500_gene_names | Random gene names |
| results | Results from running SDA on simulated 2D dataset |
| reverselog_trans | reversed log scale |
| run_SDA | run_SDA |
| scores_distribution | Plot overall distribution of individual scores |
| simulate_2D_data | Simulate 2D Data |
