# Robust statistical inference for quantitative LC-MS proteomics

## Documentation for package ‘msqrob2’ version 1.20.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

.computeNfLogMedian | Helper function to calculate sample-specific normalization factors on the log2 scale using conventional median normalisation
.computeNfLogMedianOfRatios | Helper function to calculate sample-specific normalization factors
.StatModel | The StatModel class for msqrob
createPairwiseContrasts | Construct all contrasts for all pairwise comparisons between all levels of a factor
data | Example data for 100 proteins
getCoef | Accessor functions for StatModel class
getCoef-method | Accessor functions for StatModel class
getContrast | Methods for StatModel class
getContrast-method | Methods for StatModel class
getDF | Accessor functions for StatModel class
getDF-method | Accessor functions for StatModel class
getDfPosterior | Accessor functions for StatModel class
getDfPosterior-method | Accessor functions for StatModel class
getFitMethod | Accessor functions for StatModel class
getFitMethod-method | Accessor functions for StatModel class
getModel | Accessor functions for StatModel class
getModel-method | Accessor functions for StatModel class
getSigma | Accessor functions for StatModel class
getSigma-method | Accessor functions for StatModel class
getSigmaPosterior | Accessor functions for StatModel class
getSigmaPosterior-method | Accessor functions for StatModel class
getVar | Accessor functions for StatModel class
getVar-method | Accessor functions for StatModel class
getVarPosterior | Accessor functions for StatModel class
getVarPosterior-method | Accessor functions for StatModel class
getVcovUnscaled | Accessor functions for StatModel class
getVcovUnscaled-method | Accessor functions for StatModel class
hypothesisTest | Parameter estimates, standard errors and statistical inference on differential expression analysis
hypothesisTest-method | Parameter estimates, standard errors and statistical inference on differential expression analysis
hypothesisTestHurdle | Parameter estimates, standard errors and statistical inference on differential expression analysis
hypothesisTestHurdle-method | Parameter estimates, standard errors and statistical inference on differential expression analysis
makeContrast | Make contrast matrix
msqrob | Methods to fit msqrob models with ridge regression and/or random effects using lme4
msqrob-method | Methods to fit msqrob models with ridge regression and/or random effects using lme4
msqrobAggregate | Method to fit msqrob models with robust regression and/or ridge regression and/or random effects It models multiple features simultaneously, e.g. multiple peptides from the same protein.
msqrobAggregate-method | Method to fit msqrob models with robust regression and/or ridge regression and/or random effects It models multiple features simultaneously, e.g. multiple peptides from the same protein.
msqrobCollect | Function to collect the inference tables generated by the msqrob2 statistical inference workflow.
msqrobGlm | Function to fit msqrob models to peptide counts using glm
msqrobHurdle | Function to fit msqrob hurdle models
msqrobHurdle-method | Function to fit msqrob hurdle models
msqrobLm | Function to fit msqrob models using lm and rlm
msqrobLmer | Function to fit msqrob models with ridge regression and/or random effects using lme4
msqrobQB | Function to fit msqrob models to peptide counts using glm
msqrobQB-method | Function to fit msqrob models to peptide counts using glm
nfLogMedian | Methods to computes sample-specific normalization factors on the log scale using conventional median summarisation.
nfLogMedian-method | Methods to computes sample-specific normalization factors on the log scale using conventional median summarisation.
nfLogMedianOfRatios | Methods to calculate log-scale normalization factors using the median-of-ratios method
nfLogMedianOfRatios-method | Methods to calculate log-scale normalization factors using the median-of-ratios method
pe | Example data for 100 proteins
plotVolcano | Volcano plot
show-method | The StatModel class for msqrob
smallestUniqueGroups | Smallest unique protein groups
StatModel | The StatModel class for msqrob
StatModel-class | The StatModel class for msqrob
StatModel-method | Methods for StatModel class
statModelAccessors | Accessor functions for StatModel class
statModelMethods | Methods for StatModel class
topFeatures | Toplist of DE proteins, peptides or features
varContrast | Methods for StatModel class
varContrast-method | Methods for StatModel class