Function reference • FacileAnalysis

All functions
`viz()` `shine()` `report()`	Methods to interactively explore and report FacileAnalysisResults.
`biocbox(<FacileLinearModelDefinition>)` `biocbox(<FacileDgeAnalysisResult>)`	Construct a bioconductor classed object from an analysis.
`comparable()`	Are two facile objects comparable?
`compare()`	Compares two (or more(?)) FacileAnalysisResults against each other.
`design()`	Extract the design matrix from objects used in a linear modeling step
`fDgeSeaAnalysis()`	An analysis module that combines differential expression with GESA.
`faro()`	Extract the internal (F)acile(A)nalysis(R)esult (O)bject from a container.
`fdgeGadget()` `fdgeAnalysis()`	Fully interactive differential expression analysis
`fdge()` `compare(<FacileTtestAnalysisResult>)` `tidy(<FacileTtestComparisonAnalysisResult>)` `report(<FacileTtestAnalysisResult>)` `ffsea(<FacileTtestComparisonAnalysisResult>)`	Peform a differential expression analysis.
`fdgeRun()`	Shiny module to configure and run fdge over a predefined model.
`fdgeView()`	Shiny module that interacts with result of fdgeRun module
`fdge_methods()`	A table of assay_type,dge_method combination parameters
`fdgeseaGadget()`	Gadget to run both DGE and GSEA
`ffsea()` `result(<FacileFseaAnalysisResult>)`	Performs Feature (Gene) Set Enrichment Analyses
`ffsea_methods()`	Returns the types of featureset enrichment methods available over different types of results.
`flmDefRun()`	A shiny module that generates a linear model definition via `flm_def`.
`flm_def()`	Builds (simple) design and contrast matrices for use with `fdge()`
`compare(<FacilePcaAnalysisResult>)` `fpca()`	Runs a principal components analysis, the facile way.
`fpcaGadget()`	Perform a PCA analysis on a (subset) of a FacileDataStore
`fpcaRun()`	Minimal shiny module to run fpca
`frunGadget()`	Support harness to initialize and launch a shiny gadget over a facile object.
`guess_feature_type()`	Guesses the type of identifiers provided.
`interacted()`	Extracts interactions over an object that happened in a gadget
`ffseaGadget()` `ffseaRun()`	Full interactive executation of GSEA, soup to nuts.
`model()`	Extract the model used for an analysis
`param()`	Extract the value of a parameter(s) used in a FacileAnalysis result
`ranks()`	Extracts ranks and signatures from a FacileAnalysisResult.
`refds()`	Reconstitute FacileDataStore links from unfds'd objects
`fsave()` `fload()`	Save and load FacileAnalysisResult objects to/from disk.
`signature()`	Converts an analysis result into a "signature" type of thing.
`signed()`	Are these results (ranks, signatures) signed?
`status()`	Reports the status of the AnalysisResult
`unfds()`	Strip and restore FacileDataStore pointers from/to FacileAnalysis Results
`unreact()`	Replace reactive versions of facile objects with their "inert" counterparts
`with_sample_covs()`	Retrieves sample covariates with option to use custom covariates by user.

Reference

All functions