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All functions

analyze.ma()
MA: fold change versus average abundance
analyze.mod_t()
Empirical Bayes moderated t-test
analyze.pca()
PCA: principal component analysis
analyze.plsda()
PLS-DA: partial least squares discriminant analysis
analyze.t()
Student's t-test
analyze.wilcox()
Wilcoxon test
dataMissing()
Counting missing data
filterNA()
Filtering NA's post-imputation
filterOutIn()
Filtering proteins or contaminants
filterProtein()
Filter proteins by gene, accession or description
impute.knn()
Imputation by the k-nearest neighbors algorithm
impute.knn_seq()
Imputation by the k-nearest neighbors algorithm
impute.knn_trunc()
Imputation by the truncated k-nearest neighbors algorithm
impute.mice_cart()
Imputation by classification and regression trees
impute.mice_norm()
Imputation by Bayesian linear regression
impute.min_global()
Imputation by the global minimum
impute.min_local()
Imputation by the local minimum
impute.nuc_norm()
Imputation by the nuclear-norm regularization
impute.pca_bayes()
Imputation by Bayesian principal components analysis
impute.pca_prob()
Imputation by probabilistic principal components analysis
normalize()
Normalization of preprocessed data
preprocessing()
Loading, filtering and reformatting of MS DIA data from Spectronaut
preprocessing_scaffold()
Loading and reformatting of MS data from Scaffold
pullProteinPath()
Compiling data on a single protein from each step in the process
sortcondition()
Creating a keyed list of conditions to the list of proteins that are present
summarize()
Summarize protein intensities across conditions
transform()
Transformation
trimFASTA()
Trimming down a protein FASTA file to certain proteins
visualize.biplot()
Biplot of individuals and variables
visualize.boxplot()
Boxplot
visualize.heatmap()
Heatmap
visualize.ind()
Graph of individuals
visualize.ma()
MA plot: plots fold change versus average abundance
visualize.rank()
Rank abundance distribution plot (Whittaker plot)
visualize.scree()
Scree plot
visualize.test()
Histograms of fold changes and p-values from test results
visualize.upset()
UpSet plot
visualize.var()
Graph of variables
visualize.venn()
Venn diagram
visualize.volcano()
Volcano plot