combine multiple samples from one individual into a single tree

[Gravityzd]

Hello! I'm interested in merging multiple sample data from the same individual into a single tree. using RedeemR.
Could you please provide guidance on how to achieve this?
Thanks a lot!

[chenweng1991]

Dear Gravityzd:
Thanks for your feedback. Please try the following function. We will incorporate this function into redeemR soon. Please let me know if it works for you.

Thank you!
Best regards
--Chen

## This function has two parameter, one is a list of redeemR objects (with names for each element), the other is the thr, "S", "LS", etc
combined_redeemR<-function(ob.list,thr){
    ## Combine GTsummary(Add suffix at the end of cell names)
    mutated_list <- lapply(seq_along(ob.list), function(i) {
    x <- ob.list[[i]]@GTsummary.filtered
    suffix <- paste0("_", i)
    x <- mutate(x, Cell = paste0(Cell, suffix))
    return(x)
    })
    combined.GTsummary <- do.call(rbind, mutated_list)
    ## Combine depth
    pos_cov<-ob.list[[1]]@DepthSummary[[1]][,1,drop=F]
    pos_cov$meanCov<-lapply(ob.list,function(x){x@DepthSummary[[1]][,2]}) %>% do.call(cbind,.) %>% rowSums
    ## Combine depth at cell level(Add suffix at the end of cell names)
    mutated_list <- lapply(seq_along(ob.list), function(i) {
    x <- ob.list[[i]]@DepthSummary[[2]]
    suffix <- paste0("_", i)
    x <- mutate(x, V1 = paste0(V1, suffix),Sample=names(ob.list)[i])
    return(x)
    })
    cell_cov<-do.call(rbind, mutated_list)
    combined.DepthSummary<-list(pos_cov,cell_cov)
    names(combined.DepthSummary)<-c("Pos.MeanCov","Cell.MeanCov")
    ## Add attributes
    attr(combined.GTsummary,"depth")<-combined.DepthSummary
    attr(combined.GTsummary, "thr")<-thr
    combined_redeemR<-Create_redeemR(combined.GTsummary)
    return(combined_redeemR)
}

[danielee0707]

Thank you for posting this. When I ran it on the three datasets followed by steps in Get_Started notebook, I got an error when running Show_Consensus and ComputeRejectRate steps complaining there are no RawGenotypes.Sensitive.StrandBalance files, probably because attr$path is NULL. Are these steps important?

[chenweng1991]

Dear @danielee0707
It is ok not running Show_Consensus and ComputeRejectRate. They are not essential. But we will also update when we revise this function and put into the code function in the R package. Thank you

Best
Chen