Man pages for proBatch
Tools for Diagnostics and Corrections of Batch Effects in Proteomics

calculate_feature_CVCalculate CV distribution for each feature
calculate_peptide_corr_distrCalculate peptide correlation between and within peptides of...
calculate_PVCACalculate variance distribution by variable
calculate_sample_corr_distrCalculates correlation for all pairs of the samples in data...
check_sample_consistencyCheck if sample annotation is consistent with data matrix and...
color_list_to_dfColor list to data frame
correct_batch_effectsBatch correction of normalized data
create_peptide_annotationPrepare peptide annotation from long format data frame Create...
dates_to_posixConvert data/time to POSIXct
date_to_sample_orderConvert date/time to POSIXct and rank samples by it
define_sample_orderDefining sample order internally
example_peptide_annotationPeptide annotation data
example_proteomeExample protein data in long format
example_proteome_matrixExample protein data in matrix
example_sample_annotationSample annotation data version 1
feature_level_diagnosticsPloting peptide measurements
fit_nonlinearFit a non-linear trend (currently optimized for LOESS)
generate_colors_for_numericGenerates color vector from continous palette
long_to_matrixLong to wide data format conversion
matrix_to_longWide to long conversion
merge_rare_levelsReplaces rare levels with other
normalizeData normalization methods
plot_corr_matrixVisualise correlation matrix
plot_CV_distrPlot CV distribution to compare various steps of the analysis
plot_CV_distr.dfPlot the distribution (boxplots) of per-batch per-step CV of...
plot_heatmap_diagnosticPlot the heatmap of samples (cols) vs features (rows)
plot_heatmap_genericPlot the heatmap
plot_hierarchical_clusteringcluster the data matrix to visually inspect which confounder...
plot_PCAplot PCA plot
plot_peptide_corr_distributionCreate violin plot of peptide correlation distribution
plot_protein_corrplotPeptide correlation matrix (heatmap)
plot_PVCAPlot variance distribution by variable
plot_PVCA.dfplot PVCA, when the analysis is completed
plot_sample_corr_distributionCreate violin plot of sample correlation distribution
plot_sample_corr_heatmapSample correlation matrix (heatmap)
plot_sample_mean_or_boxplotPlot per-sample mean or boxplots for initial assessment
plot_split_violin_with_boxplotPlot split violin plot (convenient to compare distribution...
prepare_PVCA_dfprepare the weights of Principal Variance Components
proBatchproBatch: A package for diagnostics and correction of batch...
sample_annotation_to_colorsGenerate colors for sample annotation
transform_raw_dataFunctions to log transform raw data before normalization and...
proBatch documentation built on April 29, 2020, 5:04 a.m.