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 |