SVCFit/NAMESPACE at main · KarchinLab/SVCFit · GitHub

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# Generated by roxygen2: do not edit by hand

export(analyze_svclone)
export(annotate_cnv)
export(apply_hemizygous_cn)
export(assign_background_cnv)
export(assign_cnv)
export(assign_svids)
export(attach_truth)
export(build_tree)
export(build_trees)
export(calcSubcloneProportions)
export(calc_svcf)
export(characterize_sv)
export(classify_cn)
export(cluster_data)
export(extract_info)
export(hemizygous_cn_conflicts)
export(hemizygous_del_svcf)
export(hemizygous_dup_svcf)
export(load_data)
export(load_truth)
export(local_ploidy)
export(parse_het_snps)
export(parse_snp_on_sv)
export(parse_sv_info)
export(plotSubclonePie)
export(plotTree)
export(proc_bnd)
export(resolve_hemizygous_svcf)
export(run_dp_gmm_pair)
export(run_svcfit)
export(solve_hemizygous_cn)
export(sum_sv_info)
export(svcf_status)
import(dplyr)
import(tidyr)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,mcols)
importFrom(GenomicRanges,pintersect)
importFrom(GenomicRanges,seqnames)
importFrom(GenomicRanges,start)
importFrom(GenomicRanges,width)
importFrom(IRanges,IRanges)
importFrom(RColorBrewer,brewer.pal)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(ggplot2,aes)
importFrom(ggplot2,coord_polar)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,theme_void)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,colors)
importFrom(graphics,par)
importFrom(reticulate,import)
importFrom(reticulate,py_config)
importFrom(stats,dist)
importFrom(stats,setNames)
importFrom(stringr,str_detect)
importFrom(utils,read.delim)
importFrom(utils,read.table)