aldex2propr             Import 'ALDEx2' Object
as_safe_matrix          Ensure Matrix Has Dim Names
calculate_theta         Calculate Theta and Related Statistics
compute_iqlr            Compute IQLR (Interquartile Range Log Ratio)
                        Features
countValuesBeyondThreshold
                        Count Values Greater or Less Than a Threshold
getAdjacencyFDR         Get Adjacency Matrix as indicated by
                        permutation tests.
getAdjacencyFstat       Get Adjacency Matrix as indicated by
                        F-statistics
getCutoffFDR            Get a meaningful cutoff based on the FDR values
                        from permutation tests.
getCutoffFstat          Calculate a theta Cutoff based on the
                        F-statistic.
getFdrRandcounts.propd.parallel
                        This function counts the permuted values
                        greater or less than each cutoff, using
                        parallel processing, for a propd object.
getFdrRandcounts.propd.run
                        This function counts the permuted values
                        greater or less than each cutoff, using a
                        single core, for a propd object.
getFdrRandcounts.propr.parallel
                        This function counts the permuted values
                        greater or less than each cutoff, using
                        parallel processing, for a propr object
getFdrRandcounts.propr.run
                        This function counts the permuted values
                        greater or less than each cutoff, using a
                        single core, for a propr object.
getMatrix               Get Matrix from Object
getMovingAverage        Caclulate the moving average of a vector.
getPermutedTheta        Get the theta values for a given permutation
getPermutedThetaMod     Get the theta mod values for a given
                        permutation
getRatios               Get (Log-)ratios from Object
getResults              Get Results from Object
getSignificantResultsFDR
                        Get Significant Results from Object based on
                        the permutation tests.
getSignificantResultsFstat
                        Get Significant Results based on the F-stats.
index_reference         Index Reference for Selecting Features
logratio                Perform log-ratio transformation
logratio_with_alpha     Perform log-ratio transformation with alpha
                        parameter
logratio_without_alpha
                        Perform log-ratio transformation without alpha
                        parameter
lrv_with_shrinkage      Calculate Logratio Variance with shrinkage
marg.abs                Example Absolute mRNA
packageCheck            Package Check
pcor.bshrink            Basis Covariance Shrinkage and Partial
                        Correlation Calculation
progress                Make Progress Bar
propd-class             The propd Method
propr-class             The propr Package
ratios                  Recast Matrix as Feature (Log-)Ratios
results_to_matrix       Get Matrix from Results
runGraflex              Calculate odds ratio and FDR
runNormalization        Get Per-Feature Theta
runPostHoc              Perform Post-Hoc Testing
search_tree             Search Tree Function
selectRatios            Pairwise Ratio Selection
selectReference         Select Optimal Reference Component
simple_zero_replacement
                        Simple Zero Replacement in a Count Matrix
updateCutoffs           Update FDR by Permutation
updatePermutes          Create permuted data
