battenberg/NAMESPACE at master · Wedge-lab/battenberg · GitHub

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# Generated by roxygen2: do not edit by hand

S3method(plot,haplotype.data)
export(GetChromosomeBAFs)
export(GetChromosomeBAFs_SNP6)
export(allele_ratio_plot)
export(battenberg)
export(calc_psi_t)
export(calc_rho_psi_refit)
export(callChrXsubclones)
export(callSubclones)
export(call_multisample_MSAI)
export(cel2baf.logr)
export(cell_line_baf_logR)
export(cell_line_reconstruct_normal)
export(cnfit_to_refit_suggestions)
export(combine.baf.files)
export(combine.impute.output)
export(convert.impute.input.to.beagle.input)
export(coverage_plot)
export(find_centroid_of_global_minima)
export(fit.copy.number)
export(gc.correct)
export(gc.correct.wgs)
export(gc.correct.wgs.germline)
export(generate.impute.input.snp6)
export(generate.impute.input.wgs)
export(generate.impute.input.wgs.germline)
export(germline_baf_logR)
export(germline_reconstruct_normal)
export(get.chrom.names)
export(getAlleleCounts)
export(getBAFsAndLogRs)
export(get_multisample_phasing)
export(infer_gender_birdseed)
export(input_known_haplotypes)
export(make_posthoc_plots)
export(parse.imputeinfofile)
export(prepare_snp6)
export(prepare_wgs)
export(prepare_wgs_cell_line)
export(prepare_wgs_germline)
export(read_table_generic)
export(run.beagle5)
export(run.impute)
export(runASCAT)
export(run_clonal_ASCAT)
export(run_haplotyping)
export(run_haplotyping_germline)
export(segment.baf.phased)
export(segment.baf.phased.legacy)
export(segment.baf.phased.multisample)
export(segment.baf.phased.sv)
export(split_input_haplotypes)
export(squaresplot)
export(standardiseChrNotation)
export(standardiseChrNotation_germline)
export(suggest_refit)
export(totalcn_chrom_plot)
export(write_battenberg_phasing)
export(writebeagle.as.impute)
export(writevcf.beagle)
import(ggplot2)
import(grDevices)
import(graphics)
import(stats)
import(utils)
importFrom(ASCAT,ascat.plotAscatProfile)
importFrom(ASCAT,ascat.plotNonRounded)
importFrom(ASCAT,ascat.plotSunrise)
importFrom(ASCAT,make_segments)
importFrom(GenomicRanges,distance)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(GenomicRanges,mcols)
importFrom(GenomicRanges,seqinfo)
importFrom(GenomicRanges,seqnames)
importFrom(GenomicRanges,start)
importFrom(GenomicRanges,width)
importFrom(RColorBrewer,brewer.pal)
importFrom(doParallel,registerDoParallel)
importFrom(foreach,"%dopar%")
importFrom(foreach,foreach)
importFrom(gridExtra,arrangeGrob)
importFrom(gridExtra,grid.arrange)
importFrom(gtools,mixedsort)
importFrom(parallel,makeCluster)
importFrom(parallel,stopCluster)
importFrom(readr,cols)
importFrom(readr,read_table)
importFrom(readr,write_tsv)
importFrom(splines,ns)