Create_redeemR

This function is to create redeemR with basic information

Create_redeemR(
  VariantsGTSummary = VariantsGTSummary,
  qualifiedCellCut = 10,
  VAFcut = 1,
  Cellcut = 2,
  maxctscut = 2
)

Arguments

VariantsGTSummary

simply put GTSummary (Generated by redeemR.read)

qualifiedCellCut

The minimum median mitochondrial coverage for a qualified cell, default is 10

VAFcut

only use variants with VAF smaller than VAFcut. Default is 1. We can use smaller value to constrain into only using rare variants

Cellcut

only use variants with at least cellcut cells carry

maxctscut

only use variants with at least in one cell with at leaset maxctscut variant fragments

OnlyHetero

If only consider the heteroplasmy variants, default is T

Value

redeemR class