proBatch-package	proBatch
adjust_batch_trend_df	correct_batch_effects
adjust_batch_trend_dm	correct_batch_effects
calculate_feature_CV	calculate_feature_CV
calculate_peptide_corr_distr	calculate_peptide_corr_distr
calculate_PVCA	calculate_PVCA
calculate_PVCA.default	calculate_PVCA
calculate_PVCA.ProBatchFeatures	calculate_PVCA
calculate_sample_corr_distr	calculate_sample_corr_distr
center_feature_batch_means_df	correct_batch_effects
center_feature_batch_means_dm	correct_batch_effects
center_feature_batch_medians_df	correct_batch_effects
center_feature_batch_medians_dm	correct_batch_effects
check_sample_consistency	check_sample_consistency
color_list_to_df	color_list_to_df
convert_annotation_classes	convert_annotation_classes
correct_batch_effects	correct_batch_effects
correct_batch_effects_df	correct_batch_effects
correct_batch_effects_dm	correct_batch_effects
correct_with_ComBat_df	correct_batch_effects
correct_with_ComBat_dm	correct_batch_effects
correct_with_removeBatchEffect_dm	correct_with_removeBatchEffect_dm
create_peptide_annotation	create_peptide_annotation
dates_to_posix	dates_to_posix
date_to_sample_order	date_to_sample_order
define_sample_order	define_sample_order
example_ecoli_data	example_ecoli_data
example_peptide_annotation	example_peptide_annotation
example_proteome	example_proteome
example_proteome_matrix	example_proteome_matrix
example_sample_annotation	example_sample_annotation
feature_level_diagnostics	feature_level_diagnostics
fit_nonlinear	fit_nonlinear
generate_colors_for_numeric	generate_colors_for_numeric
get_chain	get_chain
get_operation_log	get_operation_log
guess_factor_columns_if_needed	guess_factor_columns_if_needed
handle_factor_numeric_overlap	handle_factor_numeric_overlap
handle_missing_values	handle_missing_values
log_transform_df	transform_raw_data
log_transform_dm	transform_raw_data
log_transform_dm.default	transform_raw_data
log_transform_dm.ProBatchFeatures	transform_raw_data
long_to_matrix	long_to_matrix
matrix_to_long	matrix_to_long
merge_rare_levels	merge_rare_levels
normalize	normalize
normalize_data_df	normalize
normalize_data_dm	normalize
normalize_sample_medians_df	normalize
normalize_sample_medians_dm	normalize
pb_add_level	pb_add_level
pb_aggregate_level	pb_aggregate_level
pb_assay_matrix	pb_assay_matrix
pb_as_long	pb_as_long
pb_as_wide	pb_as_wide
pb_current_assay	pb_current_assay
pb_eval	pb_eval
pb_filterNA	pb_missing_helpers
pb_infIsNA	pb_missing_helpers
pb_missing_helpers	pb_missing_helpers
pb_nNA	pb_missing_helpers
pb_pipeline_name	pb_pipeline_name
pb_register_step	pb_register_step
pb_transform	pb_transform
pb_zeroIsNA	pb_missing_helpers
plot_boxplot	plot_sample_mean_or_boxplot
plot_boxplot.default	plot_sample_mean_or_boxplot
plot_boxplot.ProBatchFeatures	plot_sample_mean_or_boxplot
plot_corr_matrix	plot_corr_matrix
plot_CV_distr	plot_CV_distr
plot_CV_distr.df	plot_CV_distr.df
plot_heatmap_diagnostic	plot_heatmap_diagnostic
plot_heatmap_diagnostic.default	plot_heatmap_diagnostic
plot_heatmap_diagnostic.ProBatchFeatures	plot_heatmap_diagnostic
plot_heatmap_generic	plot_heatmap_generic
plot_heatmap_generic.default	plot_heatmap_generic
plot_heatmap_generic.ProBatchFeatures	plot_heatmap_generic
plot_hierarchical_clustering	plot_hierarchical_clustering
plot_hierarchical_clustering.default	plot_hierarchical_clustering
plot_hierarchical_clustering.ProBatchFeatures	plot_hierarchical_clustering
plot_iRT	feature_level_diagnostics
plot_NA_density	plot_NA_density
plot_NA_density.default	plot_NA_density
plot_NA_density.ProBatchFeatures	plot_NA_density
plot_NA_frequency	plot_NA_frequency
plot_NA_frequency.default	plot_NA_frequency
plot_NA_frequency.ProBatchFeatures	plot_NA_frequency
plot_NA_heatmap	plot_NA_heatmap
plot_NA_heatmap.default	plot_NA_heatmap
plot_NA_heatmap.ProBatchFeatures	plot_NA_heatmap
plot_PCA	plot_PCA
plot_PCA.default	plot_PCA
plot_PCA.ProBatchFeatures	plot_PCA
plot_peptides_of_one_protein	feature_level_diagnostics
plot_peptide_corr_distribution	plot_peptide_corr_distribution
plot_peptide_corr_distribution.corrDF	plot_peptide_corr_distribution
plot_protein_corrplot	plot_protein_corrplot
plot_PVCA	plot_PVCA
plot_PVCA.default	plot_PVCA
plot_PVCA.df	plot_PVCA.df
plot_PVCA.ProBatchFeatures	plot_PVCA
plot_sample_corr_distribution	plot_sample_corr_distribution
plot_sample_corr_distribution.corrDF	plot_sample_corr_distribution
plot_sample_corr_heatmap	plot_sample_corr_heatmap
plot_sample_mean	plot_sample_mean_or_boxplot
plot_sample_mean.default	plot_sample_mean_or_boxplot
plot_sample_mean.ProBatchFeatures	plot_sample_mean_or_boxplot
plot_sample_mean_or_boxplot	plot_sample_mean_or_boxplot
plot_single_feature	feature_level_diagnostics
plot_spike_in	feature_level_diagnostics
plot_split_violin_with_boxplot	plot_split_violin_with_boxplot
plot_with_fitting_curve	feature_level_diagnostics
prepare_PVCA_df	prepare_PVCA_df
prepare_PVCA_df.default	prepare_PVCA_df
prepare_PVCA_df.ProBatchFeatures	prepare_PVCA_df
proBatch	proBatch
ProBatchFeatures	ProBatchFeatures
ProBatchFeatures-class	ProBatchFeatures-class
ProBatchFeatures-subset	ProBatchFeatures-subset
ProBatchFeatures_from_long	ProBatchFeatures_from_long
quantile_normalize_df	normalize
quantile_normalize_dm	normalize
sample_annotation_to_colors	sample_annotation_to_colors
sample_annotation_to_colors.default	sample_annotation_to_colors
sample_annotation_to_colors.ProBatchFeatures	sample_annotation_to_colors
subset_keep_cols	subset_keep_cols
transform_raw_data	transform_raw_data
unlog_df	transform_raw_data
unlog_dm	transform_raw_data
unlog_dm.default	transform_raw_data
unlog_dm.ProBatchFeatures	transform_raw_data
warn_unmapped_columns	warn_unmapped_columns
[,ProBatchFeatures,ANY,ANY,ANY-method	ProBatchFeatures-subset
