panvaR/NAMESPACE at main · danforthcenter/panvaR · GitHub

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# Generated by roxygen2: do not edit by hand

export(format_snpeff_annotations)
export(get_bp_from_id)
export(get_chrom_from_id)
export(get_ld_in_window)
export(make_consistent_scale)
export(make_panvar_inputs)
export(make_panvar_tables)
export(make_scores)
export(panvar_mvp_gwas)
export(panvar_shiny)
export(plot_effect)
export(plot_gene_annotation)
export(plot_panvar)
export(plot_panvar_manhattan)
export(plot_pc_scree)
export(plotly_gene_annotation)
export(plotly_panvar)
export(plotly_panvar_manhattan)
export(set_out_dir)
export(set_panvar_prefix)
export(set_plink_path)
export(snp_make_clumps)
export(snp_qc_plink)
importFrom(bigsnpr,download_plink2)
importFrom(bigstatsr,big_univLinReg)
importFrom(bslib,tooltip)
importFrom(data.table,fread)
importFrom(dplyr,"%>%")
importFrom(dplyr,across)
importFrom(dplyr,add_row)
importFrom(dplyr,all_of)
importFrom(dplyr,arrange)
importFrom(dplyr,between)
importFrom(dplyr,bind_rows)
importFrom(dplyr,case_when)
importFrom(dplyr,contains)
importFrom(dplyr,dense_rank)
importFrom(dplyr,desc)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,last_col)
importFrom(dplyr,left_join)
importFrom(dplyr,matches)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,pull)
importFrom(dplyr,relocate)
importFrom(dplyr,rename)
importFrom(dplyr,rename_with)
importFrom(dplyr,rowwise)
importFrom(dplyr,select)
importFrom(dplyr,slice)
importFrom(dplyr,starts_with)
importFrom(dplyr,summarize)
importFrom(dplyr,ungroup)
importFrom(ggfittext,geom_fit_text)
importFrom(gggenes,geom_gene_arrow)
importFrom(ggnewscale,new_scale_color)
importFrom(ggplot2,aes)
importFrom(ggplot2,binned_scale)
importFrom(ggplot2,coord_cartesian)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_rug)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_alpha)
importFrom(ggplot2,scale_alpha_continuous)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_color_viridis_b)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_fill_viridis_b)
importFrom(ggplot2,scale_shape_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_x_reverse)
importFrom(ggplot2,scale_y_reverse)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_void)
importFrom(ggplot2,unit)
importFrom(ggplot2,xlim)
importFrom(ggplot2,ylim)
importFrom(khroma,plot_scheme)
importFrom(patchwork,plot_layout)
importFrom(pcadapt,pcadapt)
importFrom(pcadapt,read.pcadapt)
importFrom(plotly,ggplotly)
importFrom(plotly,layout)
importFrom(rMVP,MVP)
importFrom(rMVP,MVP.Data)
importFrom(rMVP,attach.big.matrix)
importFrom(rlang,.data)
importFrom(rlang,arg_match)
importFrom(stats,complete.cases)
importFrom(stats,cor.test)
importFrom(stats,median)
importFrom(stats,predict)
importFrom(stats,weighted.mean)
importFrom(stringr,str_detect)
importFrom(stringr,str_extract_all)
importFrom(stringr,str_replace)
importFrom(sys,exec_wait)
importFrom(tibble,add_column)
importFrom(tibble,enframe)
importFrom(tidyr,unnest_longer)
importFrom(utils,capture.output)
importFrom(utils,read.delim)
importFrom(utils,read.table)
importFrom(utils,setTxtProgressBar)
importFrom(utils,txtProgressBar)
importFrom(utils,write.csv)
importFrom(utils,write.table)