![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
| addFactorInteractions | Add a combination of two or more factor variables to a protData object |
| addVarFromVar | Add a variable to a protdata object based on an existing column |
| adjustNames | Adjust the names of the elements in a list of dataframes |
| contr.ltfr_MSqRob | Create A Full Set of Dummy Variables |
| countPeptides | Count the number of peptides in each group |
| cutOffPval | Find cut off for p-values enriched in values close to 1 |
| df2protdata | Data frame to protein data |
| dummyVars_MSqRob | Create A Full Set of Dummy Variables |
| dummyVars_MSqRob.default | Create A Full Set of Dummy Variables |
| fdrtool_subset | Estimate (Local) False Discovery Rates For Diverse Test Statistics |
| fit.model | Fit peptide-based models |
| getAccessions-method | Extract the accession slot of a protLM object |
| getAccessions-method | Extract the accession slot of a protdata object |
| getAnnotations-method | Extract the annotation slot of a protLM object |
| getAnnotations-method | Extract the annotation slot of a protdata object |
| getBetaVcovDf-method | Get beta, vcov, df and sigma from a generalized linear model |
| getBetaVcovDf-method | Get beta, vcov, df and sigma from a generalized linear mixed model |
| getBetaVcovDf-method | Get beta, vcov, df and sigma from an ordinary linear model |
| getBetaVcovDf-method | Get beta, vcov, df and sigma from a linear mixed model |
| getBetaVcovDfList | Get a list of beta, vcov, df and sigma from a protLM object |
| getData-method | Extract the data slot of a protdata object |
| getModels-method | Extract the model slot of a protLM object |
| getPData-method | Extract the annotation slot of a protdata object |
| getThetaVars | Get variances and degrees of freedom of model parameters |
| get_qvals | Adjust P-values for Multiple Comparisons |
| import2MSnSet | Import a file in a prespecified format and convert it to an MSnSet object |
| importDIAData | Import data independent acquisition files |
| index2Numeric | Convert index to only numeric values |
| init_ann_MQ_Excel | Initialize an annotation Excel file based on a MaxQuant peptides.txt file |
| inspect_loads_MSqRob | Inspect the variables present in a data.frame from binary file |
| length-method | Length of a protLM object |
| length-method | Length of a protdata object |
| loads_MSqRob | Loading only given variables of a data.frame from binary file |
| makeAnnotation | Create an annotation data frame |
| makeContrast | Create a contrast matrix |
| MSnSet2protdata | MSnSet to protein data |
| pasteAnnotation | Add annotations to a data frame in "long" format |
| plot_fdrtool | Make diagnostic plots for fdrtool results |
| predict.dummyVars_MSqRob | Create A Full Set of Dummy Variables |
| preprocess_generic | Preprocess MSnSet objects originating from prespecified file formats |
| preprocess_long | Preprocess data in "long" format |
| preprocess_MaxQuant | Preprocess MSnSet objects originating from MaxQuant peptides.txt files |
| preprocess_MSnSet | Preprocess MSnSet objects |
| preprocess_wide | Preprocess data in "wide" format |
| prot.p.adjust | Adjust P-values for Multiple Comparisons |
| prot.p.adjust_protwise | Adjust P-values for Multiple Comparisons per Protein |
| prot.signif | Assess significance of q-values and sort by significance |
| protdata-class | Protein Data Object - class |
| protLM-class | Protein Linear Model Object - class |
| read2MSnSet | Import a file and convert it to an MSnSet object |
| read_MaxQuant | Import a MaxQuant peptides.txt file |
| read_moFF | Import a peptides summary file produced by moFF |
| saves_MSqRob | Save the variables of a data.frame in distinct binary files |
| selectAccessions-method | Select accessions from a protdata object |
| setAccessions-method | Change the accession slot of a protLM object |
| setAccessions-method | Change the accession slot of a protdata object |
| setAnnotations-method | Change the annotation slot of a protLM object |
| setAnnotations-method | Change the annotation slot of a protdata object |
| setData-method | Change the data slot of a protdata object |
| setModels-method | Change the model slot of a protLM object |
| smallestUniqueGroups | Smallest unique protein groups |
| squeezePars | Squeeze variances and other parameters |
| squeezeThetas | Squeeze variances and other parameters |
| squeezeVarRob | Robustly Squeeze Sample Variances |
| test.ANOVA | ANOVA for multiple contrasts |
| test.contrast | Test a contrast |
| test.contrast_adjust | Test a contrast and perform FDR correction |
| test.contrast_stagewise | Perform stage-wise contrast testing |
| test.protLMcontrast | Test a contrast |
| update.lmerMod | Update lmerMod object with new thetas without changing the pointers of other objects |
| update_protLM | Update protLM object with new parameter variances and residual variances |
| [-method | Select elements from a protLM object |
| [-method | Select elements from a protdata object |