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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
S3method(plot,cnaqc)
S3method(print,cnaqc)
export("%>%")
export(CCF)
export(CNA)
export(CNA_gene)
export(Mutations)
export(Sequenza_CNAqc)
export(analyze_peaks)
export(annotate_variants)
export(as_maftools_cohort)
export(as_maftools_obj)
export(augment_with_maf)
export(augment_with_vep)
export(auto_tolerance)
export(compute_CCF)
export(detect_arm_overfragmentation)
export(get_PASS_percentage)
export(get_drivers)
export(init)
export(inspect_segment)
export(parse_Battenberg)
export(plot_CCF)
export(plot_SBS)
export(plot_arm_fragmentation)
export(plot_data_histogram)
export(plot_gw_ccf)
export(plot_gw_counts)
export(plot_gw_depth)
export(plot_gw_vaf)
export(plot_icon_CNA)
export(plot_karyotypes)
export(plot_multisample_CNA)
export(plot_peaks_analysis)
export(plot_qc)
export(plot_segment_size_distribution)
export(plot_segments)
export(plot_smoothing)
export(print.cnaqc)
export(smooth_segments)
export(split_by_chromosome)
export(subsample)
export(subset_by_minimum_CCF)
export(subset_by_segment_karyotype)
export(subset_by_segment_minmutations)
export(subset_by_segment_totalcn)
export(subset_snvs)
export(wt_mutant_alleles)
import(ggpubr)
importFrom(akima,interp)
importFrom(crayon,green)
importFrom(crayon,red)
importFrom(dplyr,arrange)
importFrom(dplyr,bind_cols)
importFrom(dplyr,bind_rows)
importFrom(dplyr,case_when)
importFrom(dplyr,desc)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,full_join)
importFrom(dplyr,group_split)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,pull)
importFrom(dplyr,rename)
importFrom(dplyr,right_join)
importFrom(dplyr,row_number)
importFrom(dplyr,rowwise)
importFrom(dplyr,sample_n)
importFrom(dplyr,select)
importFrom(dplyr,slice)
importFrom(dplyr,summarise)
importFrom(dplyr,ungroup)
importFrom(ggplot2,aes)
importFrom(ggplot2,alpha)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,geom_abline)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_blank)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_rect)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggplot_build)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_light)
importFrom(ggplot2,unit)
importFrom(ggplot2,xlim)
importFrom(ggplot2,ylim)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(graphics,hist)
importFrom(gtools,mixedsort)
importFrom(magrittr,"%>%")
importFrom(scales,percent)
importFrom(stats,complete.cases)
importFrom(stats,dbinom)
importFrom(stats,density)
importFrom(stats,glm)
importFrom(stats,integrate)
importFrom(stats,median)
importFrom(stats,qbinom)
importFrom(stats,quantile)
importFrom(stats,setNames)
importFrom(tibble,as_tibble)
importFrom(tibble,is_tibble)
importFrom(tibble,tibble)
importFrom(tidyr,pivot_wider)
importFrom(utils,capture.output)
importFrom(utils,object.size)