An R package to calculate proportionality and other measures for
compositional data
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Documentation for package ‘propr’ version 5.1.7
Help Pages
| 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. |
| getSignificantResultsFDR.propd | Get Significant Results from Object based on the permutation tests. |
| getSignificantResultsFDR.propr | 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_without_alpha | Perform log-ratio transformation without alpha parameter |
| logratio_with_alpha | Perform log-ratio transformation with 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 | The propd Method |
| propd-class | The propd Method |
| propr | The propr Package |
| 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 |
| setActive | The propd Method |
| setDisjointed | The propd Method |
| setEmergent | The propd Method |
| show-method | The propd Method |
| show-method | The propr Package |
| simple_zero_replacement | Simple Zero Replacement in a Count Matrix |
| updateCutoffs | Update FDR by Permutation |
| updateCutoffs.propd | Update FDR by Permutation |
| updateCutoffs.propr | Update FDR by Permutation |
| updateF | The propd Method |
| updatePermutes | Create permuted data |