Create_redeemR_model: Create_redeemR_model

In chenweng1991/scMitoTracing: R package for Regulatory multi-omics with Deep Mitochondrial mutation profiling

Create_redeemR_model

Description

This function is to create redeemR with basic information, modeled by binomial distribution maxctscut is removed, replaced by the modeling, will generate statistics and p value

Usage

Create_redeemR_model(
  VariantsGTSummary = VariantsGTSummary,
  qualifiedCellCut = 10,
  VAFcut = 1,
  Cellcut = 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
OnlyHetero	If only consider the heteroplasmy variants, default is T

Value

redeemR class

chenweng1991/scMitoTracing documentation built on June 9, 2025, 5:48 a.m.