DepthSummary: Function to summarize the depth (Total that passed Q30)

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

Function to summarize the depth (Total that passed Q30)

Description

This function allows you to summarize the depth

Usage

DepthSummary(path, CellSubset = NA, only_Total = T)

Arguments

path	The XX/final folder, the output from mitoV
CellSubset	A vector of ATAC cell names for subsetting, default is NA
only_Total	Default is T, Only return total depth summary. Don't care about depth in different quality filtering
Processed	Boolean variable(Default T), if true directly readRDS("depth.RDS") or, generate and saveout "depth.RDS"

Value

this returns depth which is a list of 4 list(Total/VerySensitive/Sensitive/Specific), each contains 2 df, summarize mito coverage by Pos/Cell

Examples

WD<-"/lab/solexa_weissman/cweng/Projects/MitoTracing_Velocity/SecondaryAnalysis/Donor01_CD34_1_Multiomekit/MTenrichCombine/Enrich/CW_mgatk/final"
DN1CD34_1.depth<-DepthSummary(WD,Processed = T)

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