redeemR.read: Function to read in redeemV outputs

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

Function to read in redeemV outputs

Description

This function allows you to read raw data from XX/final folder, the output from redeemV It process the data same way as CW_mgatk.read but need to specify one threadhold(thr)

Usage

redeemR.read(
  path,
  thr = "S",
  Processed = F,
  rdsname = "/VariantsGTSummary.RDS"
)

Arguments

path	The XX/final folder, the output from mitoV
thr	The thredhold of filtering T(Total),LS(Less Stringent:c=0.75,a1=2,a2=1), S(Stringent:c=0.75,a1=3,a2=2), VS(Very Stringent:c=0.75,a1=4,a2=3)"
Processed	Boolean variable (Default F), if true directly readRDS("VariantsGTSummary.RDS") or, generate and saveout "VariantsGTSummary.RDS"

Value

this returns depth which is a list of 4 df (Total/VerySensitive/Sensitive/Specific), each is a genotype summary

Examples

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

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