Man pages for PhilipBerg/PaiR
Imputation and Significance Analysis of Proteomics Data
| calc_weights | Calculate Precision Weights From Gamma Regression |
| extract_results | Extract the results from running the multiple imputations |
| filter_outliers | Filter lowly abundant features |
| Mean-Variance_Gamma_Regressions | Functions for Fitting the Mean-Variance Gamma Regression... |
| pipe | Pipe operator |
| plot_gamma_imputation | Function for plotting the gamma regression used for... |
| plot_gamma_precision | Function for plotting the gamma regression used for... |
| plot_gamma_regression | Function for plotting the mean-variance gamma regressions |
| plot_ma | Generate a MA-plot of the analysis. |
| plot_norm_box | Generates a box-plot for 'log2' transformed raw, tmm-, and... |
| psrn | Normalize data to a pseudo-reference |
| run_limma_and_lfc | Run limma and calculate LFC |
| run_pipeline | Run multiple imputation and limma |
| single_imputation | Single imputation |
| tmm | Normalization by Trimmed m Means |
| ups | Spiked-in data set of peptides |
| yeast | Spiked-in data set of reversibly oxidized cysteins |
