# Multiple Imputation for Proteomics

## Documentation for package ‘mi4p’ version 1.3

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

## Help Pages

check.conditions | Check if the design is valid
check.design | Check if the design is valid
datasim | A single simulated dataset
eBayes.mod | MI-aware Modifed eBayes Function
formatLimmaResult | Format a Result from Limma
hid.ebayes | MI-aware Modifed eBayes Function
limmaCompleteTest.mod | Computes a hierarchical differential analysis
make.contrast | Builds the contrast matrix
make.design | Builds the design matrix
make.design.1 | Builds the design matrix for designs of level 1
make.design.2 | Builds the design matrix for designs of level 2
make.design.3 | Builds the design matrix for designs of level 3
meanImp_emmeans | Multiple Imputation Estimate
mi4limma | Differential analysis after multiple imputation
mm_peptides | mm_peptides - peptide-level intensities for mouse
multi.impute | Multiple imputation of quantitative proteomics datasets
MVgen | Amputation of a dataset
norm.200.m100.sd1.vs.m200.sd1.list | A list of simulated datasets.
proj_matrix | Variance-Covariance Matrix Projection
protdatasim | Data simulation function
qData | Extract of the abundances of Exp1_R25_pept dataset
rubin1.all | First Rubin rule (all peptides)
rubin1.one | First Rubin rule (a given peptide)
rubin2.all | Computes the 2nd Rubin's rule (all peptides)
rubin2bt.all | 2nd Rubin's rule Between-Imputation component (all peptides)
rubin2bt.one | 2nd Rubin's rule Between-Imputation Component (a given peptide)
rubin2wt.all | 2nd Rubin's rule Within-Variance Component (all peptides)
rubin2wt.one | 2nd Rubin's rule Within-Variance Component (a given peptide)
sTab | Experimental design for the Exp1_R25_pept dataset
test.design | Check if xxxxxx
within_variance_comp_emmeans | Multiple Imputation Within Variance Component