API for proBatch
Tools for Diagnostics and Corrections of Batch Effects in Proteomics

Global functions
add_vertical_batch_borders Source code
adjust_batch_trend_df Man page Source code
adjust_batch_trend_dm Man page Source code
adjust_units Source code
calculate_PVCA Man page Source code
calculate_feature_CV Man page Source code
calculate_peptide_corr_distr Man page
calculate_sample_corr_distr Man page Source code
center_feature_batch_means_df Man page Source code
center_feature_batch_means_dm Man page Source code
center_feature_batch_medians_df Man page Source code
center_feature_batch_medians_dm Man page Source code
check_feature_id_col_in_dm Source code
check_rare_levels Source code
check_sample_consistency Man page Source code
color_list_to_df Man page
correct_batch_effects Man page
correct_batch_effects_df Man page Source code
correct_batch_effects_dm Man page Source code
correct_with_ComBat_df Man page Source code
correct_with_ComBat_dm Man page Source code
create_peptide_annotation Man page Source code
date_to_sample_order Man page Source code
dates_to_posix Man page Source code
define_sample_order Man page Source code
example_peptide_annotation Man page
example_proteome Man page
example_proteome_matrix Man page
example_sample_annotation Man page
feature_level_diagnostics Man page
fit_nonlinear Man page Source code
generate_colors_for_numeric Man page Source code
geom_split_violin Source code
get_sample_corr_df Source code
handle_missing_values Source code
is_batch_factor Source code
loess_regression Source code
loess_regression_opt Source code
log_transform_df Man page Source code
log_transform_dm Man page Source code
long_to_matrix Man page Source code
loocv.nw Source code
map_factors_to_colors Source code
map_numbers_to_colors Source code
matrix_to_long Man page Source code
merge_df_with_annotation Source code
merge_rare_levels Man page Source code
normalize Man page
normalize_data_df Man page Source code
normalize_data_dm Man page Source code
normalize_sample_medians_df Man page Source code
normalize_sample_medians_dm Man page Source code
optimise_bw Source code
optimise_df Source code
plot_CV_distr Man page Source code
plot_CV_distr.df Man page Source code
plot_PCA Man page Source code
plot_PVCA Man page Source code
plot_PVCA.df Man page Source code
plot_boxplot Man page Source code
plot_corr_matrix Man page Source code
plot_heatmap_diagnostic Man page Source code
plot_heatmap_generic Man page Source code
plot_hierarchical_clustering Man page Source code
plot_iRT Man page Source code
plot_peptide_corr_distribution Man page
plot_peptide_corr_distribution.corrDF Man page
plot_peptides_of_one_protein Man page Source code
plot_protein_corrplot Man page Source code
plot_sample_corr_distribution Man page Source code
plot_sample_corr_distribution.corrDF Man page Source code
plot_sample_corr_heatmap Man page Source code
plot_sample_mean Man page Source code
plot_sample_mean_or_boxplot Man page
plot_single_feature Man page Source code
plot_spike_in Man page Source code
plot_split_violin_with_boxplot Man page Source code
plot_with_fitting_curve Man page Source code
prepare_PVCA_df Man page Source code
proBatch Man page
quantile_normalize_df Man page Source code
quantile_normalize_dm Man page Source code
reg.fcn.nw Source code
rle_func Source code
run_ComBat_core Source code
sample_annotation_to_colors Man page Source code
save_ggplot Source code
transform_raw_data Man page
unlog_df Man page Source code
unlog_dm Man page Source code
proBatch documentation built on April 29, 2020, 5:04 a.m.