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 |
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