Package index • msDiaLogue

Preprocessing

preprocessing(): Loading, filtering and reformatting of MS DIA data from Spectronaut

preprocessing_scaffold(): Loading and reformatting of MS data from Scaffold

Transformation

transform(): Transformation

Filtering

filterNA(): Filtering NA's post-imputation

filterOutIn(): Filtering proteins or contaminants

Normalization

normalize(): Normalization of preprocessed data

Imputation

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

Summarization

summarize(): Summarize protein intensities across conditions

Analysis

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

Visualization

visualize.biplot(): Biplot of score (individuals) and loading (variables)

visualize.boxplot(): Boxplot

visualize.heatmap(): Heatmap

visualize.loading(): Loading plot / graph of variables

visualize.ma(): MA plot: plots fold change versus average abundance

visualize.rank(): Rank abundance distribution plot (Whittaker plot)

visualize.score(): Score plot / graph of individuals

visualize.scree(): Scree plot

visualize.test(): Histograms of fold changes and p-values from test results

visualize.upset(): UpSet plot

visualize.venn(): Venn diagram

visualize.vip(): VIP scores plot

visualize.volcano(): Volcano plot

Other useful

dataMissing(): Counting missing data

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

trimFASTA(): Trimming down a protein FASTA file to certain proteins