Package index • msDiaLogue

All functions

analyze(): Analyzing summarized data

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(): Generating visualizations for MS Data