# Generated by roxygen2: do not edit by hand

S3method(calculate_PVCA,ProBatchFeatures)
S3method(calculate_PVCA,default)
S3method(log_transform_dm,ProBatchFeatures)
S3method(log_transform_dm,default)
S3method(plot_NA_density,ProBatchFeatures)
S3method(plot_NA_density,default)
S3method(plot_NA_frequency,ProBatchFeatures)
S3method(plot_NA_frequency,default)
S3method(plot_NA_heatmap,ProBatchFeatures)
S3method(plot_NA_heatmap,default)
S3method(plot_PCA,ProBatchFeatures)
S3method(plot_PCA,default)
S3method(plot_PVCA,ProBatchFeatures)
S3method(plot_PVCA,default)
S3method(plot_PVCA,df)
S3method(plot_boxplot,ProBatchFeatures)
S3method(plot_boxplot,default)
S3method(plot_heatmap_diagnostic,ProBatchFeatures)
S3method(plot_heatmap_diagnostic,default)
S3method(plot_heatmap_generic,ProBatchFeatures)
S3method(plot_heatmap_generic,default)
S3method(plot_hierarchical_clustering,ProBatchFeatures)
S3method(plot_hierarchical_clustering,default)
S3method(plot_sample_mean,ProBatchFeatures)
S3method(plot_sample_mean,default)
S3method(prepare_PVCA_df,ProBatchFeatures)
S3method(prepare_PVCA_df,default)
S3method(sample_annotation_to_colors,ProBatchFeatures)
S3method(sample_annotation_to_colors,default)
S3method(unlog_dm,ProBatchFeatures)
S3method(unlog_dm,default)
export(ProBatchFeatures)
export(ProBatchFeatures_from_long)
export(adjust_batch_trend_df)
export(adjust_batch_trend_dm)
export(calculate_PVCA)
export(calculate_feature_CV)
export(calculate_peptide_corr_distr)
export(calculate_sample_corr_distr)
export(center_feature_batch_means_df)
export(center_feature_batch_means_dm)
export(center_feature_batch_medians_df)
export(center_feature_batch_medians_dm)
export(check_sample_consistency)
export(convert_annotation_classes)
export(correct_batch_effects_df)
export(correct_batch_effects_dm)
export(correct_with_ComBat_df)
export(correct_with_ComBat_dm)
export(correct_with_removeBatchEffect_dm)
export(create_peptide_annotation)
export(date_to_sample_order)
export(dates_to_posix)
export(define_sample_order)
export(fit_nonlinear)
export(generate_colors_for_numeric)
export(get_chain)
export(get_operation_log)
export(guess_factor_columns_if_needed)
export(handle_factor_numeric_overlap)
export(handle_missing_values)
export(log_transform_df)
export(log_transform_dm)
export(long_to_matrix)
export(matrix_to_long)
export(merge_rare_levels)
export(normalize_data_df)
export(normalize_data_dm)
export(normalize_sample_medians_df)
export(normalize_sample_medians_dm)
export(pb_add_level)
export(pb_aggregate_level)
export(pb_as_long)
export(pb_as_wide)
export(pb_assay_matrix)
export(pb_current_assay)
export(pb_eval)
export(pb_filterNA)
export(pb_infIsNA)
export(pb_nNA)
export(pb_pipeline_name)
export(pb_register_step)
export(pb_transform)
export(pb_zeroIsNA)
export(plot_CV_distr)
export(plot_CV_distr.df)
export(plot_NA_density)
export(plot_NA_frequency)
export(plot_NA_heatmap)
export(plot_PCA)
export(plot_PVCA)
export(plot_PVCA.df)
export(plot_boxplot)
export(plot_corr_matrix)
export(plot_heatmap_diagnostic)
export(plot_heatmap_generic)
export(plot_hierarchical_clustering)
export(plot_iRT)
export(plot_peptide_corr_distribution)
export(plot_peptide_corr_distribution.corrDF)
export(plot_peptides_of_one_protein)
export(plot_protein_corrplot)
export(plot_sample_corr_distribution)
export(plot_sample_corr_distribution.corrDF)
export(plot_sample_corr_heatmap)
export(plot_sample_mean)
export(plot_single_feature)
export(plot_spike_in)
export(plot_split_violin_with_boxplot)
export(plot_with_fitting_curve)
export(prepare_PVCA_df)
export(quantile_normalize_df)
export(quantile_normalize_dm)
export(sample_annotation_to_colors)
export(unlog_df)
export(unlog_dm)
export(warn_unmapped_columns)
exportClasses(ProBatchFeatures)
exportMethods("[")
import(QFeatures)
import(SummarizedExperiment)
import(dplyr)
import(ggfortify)
import(ggplot2)
import(lazyeval)
import(methods)
import(reshape2)
importClassesFrom(S4Vectors,DataFrame)
importFrom(Biobase,AnnotatedDataFrame)
importFrom(Biobase,ExpressionSet)
importFrom(RColorBrewer,brewer.pal)
importFrom(RColorBrewer,brewer.pal.info)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,rbind)
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(WGCNA,plotDendroAndColors)
importFrom(WGCNA,standardColors)
importFrom(corrplot,corrplot.mixed)
importFrom(data.table,setnames)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(grDevices,png)
importFrom(grid,grid.draw)
importFrom(grid,grid.newpage)
importFrom(grid,grobTree)
importFrom(gridExtra,arrangeGrob)
importFrom(gridExtra,grid.arrange)
importFrom(limma,removeBatchEffect)
importFrom(lubridate,is.POSIXct)
importFrom(magrittr,"%>%")
importFrom(matrixStats,colMedians)
importFrom(matrixStats,rowMedians)
importFrom(methods,callNextMethod)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,setClass)
importFrom(methods,setMethod)
importFrom(methods,setValidity)
importFrom(pheatmap,pheatmap)
importFrom(preprocessCore,normalize.quantiles)
importFrom(purrr,compact)
importFrom(purrr,map)
importFrom(purrr,negate)
importFrom(purrr,pmap)
importFrom(pvca,pvcaBatchAssess)
importFrom(rlang,"!!!")
importFrom(rlang,"!!")
importFrom(rlang,":=")
importFrom(rlang,.data)
importFrom(rlang,as_label)
importFrom(rlang,get_expr)
importFrom(rlang,sym)
importFrom(rlang,syms)
importFrom(scales,brewer_pal)
importFrom(scales,zero_range)
importFrom(stats,as.formula)
importFrom(stats,complete.cases)
importFrom(stats,cor)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,ksmooth)
importFrom(stats,loess)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,prcomp)
importFrom(stats,predict)
importFrom(stats,reformulate)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(sva,ComBat)
importFrom(tibble,column_to_rownames)
importFrom(tibble,remove_rownames)
importFrom(tibble,rownames_to_column)
importFrom(tibble,tibble)
importFrom(tidyr,complete)
importFrom(tidyr,nest)
importFrom(tidyr,unnest)
importFrom(tools,file_ext)
importFrom(utils,combn)
importFrom(utils,head)
importFrom(utils,tail)
importFrom(viridis,viridis_pal)
importFrom(wesanderson,wes_palettes)
