Function reference • RexMS

All functions
`BRD4_apo`	This is data to be included in my package
`BRD4_ibet`	This is data to be included in my package
`EFDR()`	Function to calculate the corresponding expected False discovery rate (eFDR) for a given threshold
`LXRalpha_compounds`	This is data to be included in my package
`LXRalpha_processed`	This is data to be included in my package
`chains()` `show(<RexParams>)` `show(<RexChain>)` `show(<RexSummary>)` `length(<RexChains>)` `length(<RexParams>)` `posteriorEstimates()` `Rex.quantiles()` `Rex.resolution()` `Rex.peptideError()` `Rex.globals()` `[[`(<RexChains>,<ANY>,<ANY>) `[`(<RexChains>,<ANY>,<ANY>,<ANY>) `[`(<RexParams>,<ANY>,<ANY>,<ANY>) `show(<RexChains>)` `show(<RexDifferential>)` `Rex.predictionError()` `Rex.estimates()` `Rex.probs()` `Rex.eFDR()`	Infrastructure to to store and process MCMC results
`TRE_dist`	This is data to be included in my package
`UnsupervisedCSA()`	Funcition for performing unsupervised conformational signature analysis. This performs PCA on the TRE values of the RexDifferentialList and returns the PCA object and the TRE values in wide format.
`cleanHDX()`	Function that checks a hdx-ms dataset for correct formatting and will clean up the dataset if specified
`cleanLong()`	Helper function to clean up long vectors
`coverageHeatmap()`	Plot a coverage heatmap
`doublelogisticFunction()`	Implementation of double logistic function (a mixture of logistics)
`error_prediction()`	Function that computes errors between the predicted peptide values and the observed peptide values
`initialiser()`	Initialiser
`logisticFunction()`	Implementation of stretched logistic function
`loglik()`	loglikelihood function for current state of parameters
`marginalEffect()`	Function to sample uncertainty of the Uptake
`maxUptakes()`	Function that compuate the maximum uptakes for all sequences in the dataset
`metropolisPi()`	metroplis step for the mixing parameter
`metropolisRate()`	Metropolis step for the rate parameters
`metropolisSigma()`	Perform a metropolis step for the variance parameter
`metropolisStretch()`	Metroplis step for the stretch parameter
`metropolisdRate()`	Metropolis step for second rate parameter
`out_lxr_compound_proccessed`	This is data to be included in my package
`define_color_function()` `hdx_to_pdb_colours()` `view_structure()`	Function to set colour ranges for HDX data visualisation onto a pdb structure
`plotButterfly()`	Rex butterfly plots for differential analysis
`plotLoadingSCSA()`	Function to plot the loading of the supervised conformational signature analysis results
`plotLogLikelihoods()`	plot loglikelihoods across chains
`plotPeptideError()`	Plot Peptide level error rates
`plotResidueResolution()`	Plot Residue level error rates to identify points where modelling is poor
`plotSCSA()`	Function to plot the supervised conformational signature analysis results
`plotSigma()`	plot sigmas across chains
`plotTREuncertainty()`	Function to plot the uncertainty in the TRE values for different states e.g. ligands. Typically used to obtain uncertainty in the conformational landscape.
`plotTREuncertaintyLoadings()`	Function to plot the uncertainty in the loading in the conformational landscape. Typically used to obtain uncertainty in the conformational signatures.
`plotTimeAveragedButterfly()`	Rex time averaged butterfly plots for differential analysis
`plotUCSA()`	Function to plot the PCA results from the UnsupervisedCSA function
`plotUptake()`	Plot the uptake from the output of a Rex model from the uptakePredict function
`plotUptakeUncertainty()`	Function to plot the uncertainty of the Uptake
`plotVolcano()`	Rex volcano plots for differential analysis
`prepareIndexes()`	Function that prepares exchange indexes for a given sequence
`processDifferential()`	Functions for differential analysis of HDX-MS data
`processTREuncertainty()`	Function to obtain uncertainty estimates for the total relative error (TRE)
`reversibleJumpBreakPointsAdd()`	Reversible jump step for adding the breakpoints
`reversibleJumpBreakPointsRemove()`	Reversible jump step for removing the breakpoints
`RexProcess()`	proccess Rex results
`rex()` `resolver()`	residue-resolved HDX-MS data analysis using Rex
`rex_lxr`	This is data to be included in my package
`sampleTREuncertainty()`	Function to calculate the uncertainty in the TRE values by sampling the posterior distribution of the Rex parameters. Typically used to obtain uncertainty in the conformational signatures.
`supervisedCSA()`	Function to perform supervised conformational signature analysis. In this case the construction of the signatures using labels as part of the dimensionality reduction which are defined in labels. The type of the labels can be catagorical or continuous. The function returns the OPLS-DA object. The labels are allowed to contain "Unknown" values which are ignored in the analysis if the type is catagorical. If the type is continuous, the "Unknown" values should be recorded as NAs.
`uptakeGuess()`	uptakeGuess
`uptakePredict()`	Function that predict the uptake from the parameters of a Rex model

Reference

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