This function is to create redeemR with basic information
Usage
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