Create_mitoTracing: Create_mitoTracing

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

Create_mitoTracing

Description

This function is to create redeemR with basic information

Usage

Create_mitoTracing(
  GTsummary_list,
  depth_list,
  feature.list_list,
  meta_list,
  labels,
  thr = "VerySensitive",
  qualifiedCellCut = 10,
  OnlyHetero = T,
  VAFcut = 1,
  Cellcut = 2,
  maxctscut = 2
)

Arguments

GTsummary_list	simply put GTSummary (Generated by CW_mgatk.read) into list, this allows mergeing multiple dataset this way.
depth_list	simply put depth(Generated by DepthSummary) into list, this allows mergeing multiple dataset this way.
feature.list_list	simply put feature.list(Generated by Vfilter_v3) into list, this allows mergeing multiple dataset this way.
labels	a vector of labels for the samples.
thr	One of the following "Total","VerySensitive","Sensitive","Specific"
qualifiedCellCut	The minimum median mitochondrial coverage for a qualified cell, default is 10
OnlyHetero	If only consider the heteroplasmy variants, default is T
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

Value

redeemR class

chenweng1991/scMitoTracing documentation built on July 2, 2024, 8:41 p.m.