# Tools for Diagnostics and Corrections of Batch Effects in Proteomics

## Documentation for package ‘proBatch’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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