NAMESPACE

# Generated by roxygen2: do not edit by hand

S3method("%Q%",CompressedGRangesList)
S3method("%Q%",GRanges)
S3method("%Q%",GRangesList)
export("%=%")
export("%K%")
export("%Q%")
export("%inn%")
export("%nin%")
export("colnames2<-")
export("names2<-")
export("rownames2<-")
export(.filter_sv)
export(.gc)
export(AND)
export(DIM)
export(DIM2)
export(NCOL2)
export(OR)
export(aggregate_roc)
export(alt_in_cis)
export(appendEnv)
export(asdf)
export(asdt)
export(asm)
export(asn2)
export(ave2)
export(ave3)
export(aved)
export(bcfindex)
export(bedpe2grl)
export(behomology)
export(binom.conf)
export(bool)
export(bp2grl)
export(cenv)
export(check_lst)
export(classystat)
export(clobber)
export(coalesce)
export(col2rn)
export(colexists)
export(colnames2)
export(column_to_rownames)
export(complete.cases2)
export(conform_si)
export(copy)
export(copy2)
export(copy3)
export(copydt)
export(copyr6)
export(copys4)
export(dcast.count)
export(dcast.count2)
export(dcast.wrap)
export(debug.s4)
export(dedup.cols)
export(df2gr)
export(df2grl)
export(dg)
export(dig_dir)
export(dig_dir2)
export(dig_job)
export(diginjob)
export(digjob)
export(dir2)
export(dirfind)
export(do.assign)
export(do.cols)
export(do.pp)
export(dodo.call2)
export(dt_any2lg)
export(dt_empty2na)
export(dt_f2char)
export(dt_lg2int)
export(dt_na2empty)
export(dt_na2false)
export(dt_na2true)
export(dt_na2zero)
export(dt_setallna)
export(dt_setchar)
export(dt_setint)
export(dt_setnull)
export(dtapply)
export(dunlist2)
export(duped)
export(dynget)
export(eNROW)
export(empty2na)
export(en2DF)
export(enframe)
export(enframe_list)
export(errr)
export(est_snv_cn)
export(est_snv_cn_stub)
export(et)
export(extract_ggplot)
export(ez_string)
export(f2int)
export(false2na)
export(feature_importance)
export(file.exists2)
export(file.info2)
export(file.mat.exists)
export(file.not.exists)
export(fillby)
export(find_dups)
export(findov)
export(fit.cnv.sig)
export(fit_classifier)
export(fitcvglmnet)
export(fitglmnet)
export(fitrandomforest)
export(fitzscore)
export(fix.cols)
export(flag2int)
export(force2)
export(forceall)
export(forcefun)
export(forceload)
export(frac)
export(g)
export(g2)
export(gbar.error)
export(gd)
export(get_accuracy)
export(get_pred)
export(getbp)
export(getcache)
export(getdat)
export(getdat2)
export(gg.hist)
export(gg.sline)
export(gg_mytheme)
export(ggmroc)
export(glm.nb2)
export(glmnet_aic)
export(globasn)
export(good.file)
export(gr.disjoin)
export(gr.fixseq)
export(gr.flipstrand)
export(gr.genome)
export(gr.noval)
export(gr.order)
export(gr.patch)
export(gr.resize)
export(gr.round)
export(gr.setdiff2)
export(gr.sort)
export(gr.splgaps)
export(gr.split)
export(gr.sprange)
export(gr.spreduce)
export(gr.strand)
export(gr.sub2)
export(gr.within)
export(gr2bed)
export(gr2df)
export(gr_calc_cov)
export(gr_construct_by)
export(gr_deconstruct_by)
export(grab.hrdetect.features)
export(grabcov)
export(grabggtrack)
export(grabhjab)
export(grep_col_sort)
export(grep_order)
export(grg_sub)
export(grl.disjoin)
export(grl.flip)
export(grl.flipstrand)
export(grl.undf)
export(grl2bedpe)
export(grok_vcf)
export(gt.each)
export(gt.fix)
export(gw_edges)
export(gx)
export(iderr)
export(idj)
export(integer_breaks)
export(interaction2)
export(interbp_dist)
export(intercalate)
export(intercalate_lst)
export(is.empty)
export(isNA)
export(isv2grl)
export(ix_sdiff)
export(jitter2)
export(kcpdf)
export(kpdf)
export(kpng)
export(ksvg)
export(lapply_dt)
export(lbl.gg)
export(len)
export(lens)
export(levelsinuse)
export(lg2f)
export(log10p)
export(loop_grep)
export(loop_grepl)
export(lst.empty)
export(lst.empty2na)
export(lst.empty2null)
export(lst.empty2zero)
export(lst.emptychar2na)
export(lst.emptychar2null)
export(lst.emptyreplace)
export(lst.null2na)
export(lst.zerochar2empty)
export(main)
export(make_chunks)
export(make_dummy)
export(make_roc)
export(make_roc2)
export(make_ttsplit)
export(make_xfold)
export(map_fus2unfus)
export(match)
export(match2)
export(match3)
export(match_s)
export(matrify)
export(matrify2)
export(max.col.narm)
export(merge.repl)
export(metanames)
export(min.col.narm)
export(mkst)
export(mrocdat)
export(mroclab)
export(mrocpred)
export(mstrsplit)
export(mylambdas)
export(mysep)
export(na.seql)
export(na2empty)
export(na2false)
export(na2true)
export(na2zero)
export(names2)
export(nan2zero)
export(ne)
export(ne.na)
export(nodim)
export(nonacol)
export(nonzero2na)
export(normpath)
export(normv)
export(normv_sep)
export(nott)
export(numeq)
export(off_diag)
export(one_vs_other)
export(output_cols)
export(overwriteR6)
export(overwritefun)
export(pairs.collect.junctions)
export(pairs.diagnose.jabba)
export(pairs.filter.sv)
export(pairs.get.jabba.pp)
export(pairs.grab.hrdetect.features)
export(pairs.grab.ot.features)
export(pairs.jabba.opt.report)
export(pairs.plot.jabba)
export(pairs.process.events)
export(pairs.process.homeology)
export(pairs.process.rbp)
export(parasn)
export(parse.gr2)
export(parse.grl2)
export(parse_slurm_time)
export(parsesnpeff)
export(peepr6)
export(pg_mytheme)
export(pinch)
export(pinch.frac)
export(plot.jabba)
export(ppdf)
export(ppng)
export(predict.pp)
export(printerr)
export(process_alt_for_hrd)
export(process_alterations)
export(process_for_rbp)
export(process_tbl)
export(qmat)
export(qq)
export(qtrim)
export(ra.dedup6)
export(ra.overlaps6)
export(rand.string)
export(read.bam.header)
export(read.header)
export(read_bed)
export(read_vcf2)
export(readin)
export(readinfasta)
export(reassign)
export(refactor)
export(rematch)
export(rep_each)
export(rep_len)
export(rep_len2)
export(replace2)
export(replace_na)
export(reset.job)
export(ret_err)
export(ret_na_err)
export(ret_no_err)
export(rg_sub)
export(rintersect)
export(rleseq)
export(rm_mparen)
export(rmcol)
export(rn2col)
export(robust.scale)
export(row.sort)
export(rownames2)
export(rownames_to_column)
export(rows.all)
export(rows.any)
export(rrrepeated)
export(runion)
export(sampler)
export(save.r)
export(seevar)
export(select.matrix)
export(selfname)
export(seq_along2)
export(setAllNames)
export(setColnames)
export(setNames2)
export(setRownames)
export(set_rngseed)
export(setcolnames)
export(setcols)
export(setrownames)
export(shift_down)
export(shift_left)
export(shift_right)
export(shift_up)
export(silent)
export(sim.bx)
export(softmax)
export(somejit)
export(split_by)
export(ss)
export(sstat)
export(stack.dt)
export(stackenv)
export(stackenv2)
export(std.calc.cov)
export(subgr)
export(subset2)
export(summ_glm)
export(sv_filter)
export(symdiff)
export(system3)
export(table2)
export(table3)
export(tailf)
export(trans)
export(trans.df)
export(transp)
export(try2)
export(un)
export(unI)
export(uncut)
export(undebug.s4)
export(undup)
export(uniqf)
export(upset2)
export(vcf_remove_sample)
export(viewtask)
export(vmatch)
export(w.quantile)
export(whicherr)
export(withv)
export(withx)
export(write.ctab)
export(write_bed)
export(ws2und)
export(wv)
export(zscore)
exportMethods(gaps)
exportMethods(within)
importFrom(GenomeInfoDb,"seqinfo<-")
importFrom(GenomeInfoDb,"seqlengths<-")
importFrom(GenomeInfoDb,"seqlevels<-")
importFrom(GenomeInfoDb,"seqnames<-")
importFrom(GenomeInfoDb,Seqinfo)
importFrom(GenomeInfoDb,seqinfo)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,seqnames)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,as.data.frame)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,split)
importFrom(S4Vectors,with)
importFrom(data.table,":=")
importFrom(data.table,as.data.table)
importFrom(data.table,dcast.data.table)
importFrom(data.table,key)
importFrom(data.table,rbindlist)
importFrom(data.table,setkey)
importFrom(data.table,setkeyv)
importFrom(data.table,setnames)
importFrom(dplyr,"%>%")
importFrom(gUtils,"%&%")
importFrom(ggplot2,aes)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_errorbar)
importFrom(ggplot2,geom_hex)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_path)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,position_dodge)
importFrom(ggplot2,rel)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_colour_manual)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(methods,setClass)
importFrom(methods,setGeneric)
importFrom(methods,setMethod)
importFrom(methods,setRefClass)