batch.neutralize        Batch effects correction
count.stats             Summary of statistics of spectral counts by
                        sample in the dataset
counts.hc               Hierarchical clustering on an spectral counts
                        matrix.
counts.heatmap          Heatmap of an spectral counts matrix.
counts.pca              Principal components analysis of an spectral
                        counts matrix.
disp.estimates          Residual dispersion estimates
filter.flags            Flag proteins with a minimum signal and/or
                        sufficient dispersion.
gene.table              Gene symbols associated to protein accessions
msms.dataset            LC-MS/MS dataset
msmsEDA-package         Exploratory Data Analysis of label-free
                        LC-MS/MS spectral counts
norm.counts             Spectral counts matrix normalization
pnms                    Accessions and gene symbols
pp.msms.data            Spectral counts matrix pre-processing
spc.barplots            Set of SpC barplots by sample
spc.boxplots            Set of SpC boxplots by sample
spc.densityplots        SpC density plots of a SpC matrix
spc.scatterplot         Scatterplot of SpC means comparing two
                        conditions
