Vfilter_v3: Function to filter variants, deprecated

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

Function to filter variants, deprecated

Description

This function allows you to filter variants,deprecated, use Vfilter_v4 instead

Usage

Vfilter_v3(
  InputSummary,
  depth,
  Rmvhomo = F,
  Min_Cells = 2,
  Max_Count_perCell = 2,
  QualifyCellCut = 10
)

Arguments

InputSummary	The GTSummary file read in by function CW_mgatk.read
depth	The .depth file by function DepthSummary
Rmvhomo	Boolean (Default F) If true, remove the homozygous variants
Min_Cells	Default 2, A qualified variant needs the minimum number of cells that have this variant
Max_Count_perCell	Default 2, A qualified variant needs to show at least 2 counts in one cell
QualifyCellCut	Default 10, Minimum depth for a qualified cell

Value

this returns feature.list

Examples

DN1CD34_1.Variants.feature.lst<-Vfilter_v3(InputSummary=DN1CD34_1.VariantsGTSummary,depth=DN1CD34_1.depth)

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