build_default_cn_list: Build default references

In TearsWillFall/ULPwgs: An implementation of a wrapper for estimating tumor fraction in ultra-low-pass whole genome sequencing (ULP-WGS) for cell-free DNA in GNU/Unix based systems

Build default references

Description

Build default references

Usage

build_default_cn_list(
  cn_list = list(cn = c("Unb.Gain", "wt", "CNNL", "NoImb_WTGrayZoneCN", "Likely Loss",
    "HemiDel", "Imb_WTGrayZoneCN", "Bal.Gain", "Likely Gain", "Uncertain Bal.Gain",
    "HomoDel", "Uncertain HomoDel", "Deletion on chrX"), cn_class = c("Gain", "Wt", "Wt",
    "Wt", "Loss", "Loss", "Wt", "Gain", "Gain", "Gain", "Loss", "Loss", "Loss"),
    class_col = c("#FF0000", "#CDCDCD", "#CDCDCD", "#CDCDCD", "#00B0F0", "#00B0F0",
    "#CDCDCD", "#FF0000", "#FF0000", "#FF0000", "#00B0F0", "#00B0F0", "#00B0F0"), col =
    c("#ED7D31", "#CDCDCD", 
     "#FFE699", "#CDCDCD", "#00B0F0", "#94F6F6", "#CDCDCD",
    "#C00000", "#FF0000", "#C00000", "#0070C0", "#0070C0", "#305496"), alpha = c(1, 0.75,
    1, 1, 1, 1, 1, 1, 1, 0.75, 1, 0.75, 0.75), order = c(3, 0, 10, 1, -2, -3, -1, 5, 2,
    4, -5, -4, -10))
)

Arguments

cn_list

List cn events

TearsWillFall/ULPwgs documentation built on April 18, 2024, 3:45 p.m.