dftdLowCov/NAMESPACE at master · TransmissibleCancerGroup/dftdLowCov · GitHub

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# Generated by roxygen2: do not edit by hand

export(clade_colours)
export(coverage_depth_summary)
export(do_simulation)
export(get_aberrant_copy_number_per_sample)
export(get_depth)
export(is.overlap)
export(isCarcinoma)
export(isCellLine)
export(isDFT1)
export(isDFT2)
export(isMarker5)
export(isMultiGain)
export(isMultiLoss)
export(isNonDFTD)
export(is_variant_site)
export(load_chromosome_lengths)
export(load_cnv_table)
export(load_sample_table)
export(load_subject_from_finalised_cnvs)
export(make_coordinates)
export(make_presence_absence_table)
export(make_segmatch)
export(pad)
export(parse_aberrant_copy_number_states)
export(parse_sample_cnv_group)
export(parse_sample_cnv_group_and_count)
export(parse_sample_cnv_group_with_clade)
export(plot_chromosome_map)
export(preprocess_for_simulation)
export(rectangle_packing4)
export(scan_col)
export(split_chars)
export(write_fasta)
importFrom("IRanges",IRanges)
importFrom("IRanges",disjoin)
importFrom("data.table",as.data.table)
importFrom("data.table",copy)
importFrom("data.table",data.table)
importFrom("data.table",foverlaps)
importFrom("data.table",key)
importFrom("data.table",melt.data.table)
importFrom("data.table",rbindlist)
importFrom("data.table",setDT)
importFrom("data.table",setkey)
importFrom("data.table",setkeyv)
importFrom("data.table",setorder)
importFrom("ggplot2",aes)
importFrom("ggplot2",geom_point)
importFrom("ggplot2",ggplot)
importFrom("ggplot2",ggtitle)
importFrom("ggplot2",scale_fill_manual)
importFrom("ggplot2",theme_classic)
importFrom("ggplot2",xlab)
importFrom("ggplot2",ylab)
importFrom("logging",logwarn)
importFrom("naturalsort",naturalsort)
importFrom("openxlsx",read.xlsx)