Tools for Diagnostics and Corrections of Batch Effects in Proteomics


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Documentation for package ‘proBatch’ version 1.0.0

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proBatch-package proBatch: A package for diagnostics and correction of batch effects, primarily in proteomics
adjust_batch_trend adjust batch signal trend with the custom (continuous) fit
center_peptide_batch_medians Median centering of the peptides (per batch median)
correct_batch_effects Batch correction method allows correction of continuous sigal drift within batch and discrete difference across batches.
correct_with_ComBat Adjusts for discrete batch effects using ComBat
create_peptide_annotation Prepare peptide annotation from long format data frame Create light-weight peptide annotation data frame for selection of illustrative proteins
dates_to_posix Convert data/time to POSIXct
date_to_sample_order Convert date/time to POSIXct and rank samples by it
example_peptide_annotation Peptide annotation data
example_proteome Example protein data in long format
example_proteome_matrix Example protein data in matrix
example_sample_annotation Sample annotation data version 1
log_transform Log transformation of the data, ensuring that the row and column names are retained
long_to_matrix Long to wide conversion
matrix_to_long Wide to long conversion
normalize Data normalization methods
normalize_data Normalization brings the samples to the same scale
normalize_sample_medians Normalization by centering sample medians to global median of the data
plot_boxplot Plot per-sample mean or boxplot (showing median and quantiles) vs order (if the real running order available)
plot_heatmap Plot the heatmap of samples
plot_hierarchical_clustering cluster the data matrix to visually inspect which confounder dominates
plot_iRT Plot iRT measurements
plot_PCA plot PCA plot
plot_peptides_of_one_protein Plot peptides of one protein
plot_peptide_corr_distribution Plot distribution of peptide correlations within one protein and between proteins
plot_protein_corrplot Peptide correlation matrix (heatmap)
plot_PVCA Plot variance distribution by variable
plot_sample_corr_distribution Create violin plot of correlation distribution
plot_sample_corr_heatmap Sample correlation matrix (heatmap)
plot_sample_mean Plot per-sample mean or boxplot (showing median and quantiles) vs order (if the real running order available)
plot_sample_mean_or_boxplot Plot per-sample mean or boxplot (showing median and quantiles) vs order (if the real running order available)
plot_single_feature Plot peptide measurements
plot_spike_in Plot spike-in measurements
plot_with_fitting_curve Plot peptide measurements across multi-step analysis
proBatch proBatch: A package for diagnostics and correction of batch effects, primarily in proteomics
quantile_normalize Quantile normalization of the data, ensuring that the row and column names are retained
sample_annotation_to_colors Generate colors for sample annotation
sample_color_scheme Sample color annotation