MBimpute                Model-Based Imputation of missing values
convert_log2            Convert values in a matrix to log2 transfored
                        values
eig_norm1               Identify bias trends
eig_norm2               EigenMS normalization
eigen_pi                Compute PI - proportion of observations missing
                        completely at random
g.test                  G Test for presence - absence analysis
get_presAbs_prots       Get Presence/Absence Proteins
hs_peptides             hs_peptides - peptide-level intensities for
                        human
makeLMFormula           String linear model formula suitable
make_intencities        Subdivide data into intensities columns only
make_meta               Subdivide data into metadata columns only
mm_peptides             mm_peptides - peptide-level intensities for
                        mouse
peptideLevel_DE         Model-Based differential expression analysis
peptideLevel_PresAbsDE
                        Presence/Absence peptide-level analysis
plot_1prot              Plot trends for a single protien
plot_3_pep_trends_NOfile
                        Plot peptide trends
plot_volcano            Volcano plot
plot_volcano_wLab       Volcano plot with labels for the differentially
                        expressed proteins
prot_level_multiMat_PresAbs
                        Multi-Matrix Presence Absence analysis
prot_level_multi_part   Multi-Matrix Differentia Expression Analysis
subset_proteins         Subset proteins
sva.id                  Surrogate Variable Analysis
