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