Man pages for marchinilab/SDAtools
SDAtools: A toolkit for SDA

check_convergenceCheck Convergence
check_simulation_scorescheck_simulation_scores
export_dataExport data and labels
genome_loadingsPlot Component Loadings by Genomic Location
get.locationLoad genomic locations from biomart
highest_componentsWhich component has the highest loading for a given gene
highest_genesWhich gene has the highest loading for a given component
load_gene_locationsLoad gene coordinates from Ensembl biomart or Cached data
loading_distributionPlot overall distribution of gene loadings
load_resultsRead SDA output into R list
PIP_component_distributionPlot PIP distribution for a single component
PIP_distributionPlot PIP distribution
PIP_threshold_distributionPlot faction PIP < 0.5 distribution
plot_free_energyPlot free energy over time
plot_free_energy_changePlot change in free energy over time
plot_loadingsPlot loadings matrices
plot_maximumsPlot maximum score and loading by component
plot_PIPPlot PIP fraction <0.5 by iteration
plot_scoresPlot Individual Scores
plot_screeScree Plot
random_500_gene_namesRandom gene names
resultsResults from running SDA on simulated 2D dataset
run_SDArun_SDA
scores_distributionPlot overall distribution of individual scores
simulate_2D_dataSimulate 2D Data
marchinilab/SDAtools documentation built on June 14, 2018, 10:20 a.m.