Function to read in mitoV outputs — redeemR.read • redeemR

This function allows you to read raw data from XX/final folder, the output from mitoV

redeemR.read(path, thr = "S", Processed = F)

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)
#> Error in CW_mgatk.read(WD, Processed = T): could not find function "CW_mgatk.read"