From a79d4a1fc3648a9e112a243fda986af2dd04f65c Mon Sep 17 00:00:00 2001 From: cweng Date: Thu, 14 Dec 2023 21:00:12 -0500 Subject: [PATCH] Add_DepthMatrix can directly give the QualifiedTotalCts as a parameter --- R/BuidTree.R | 4 +++- man/Add_DepthMatrix-redeemR-method.Rd | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/R/BuidTree.R b/R/BuidTree.R index c2d247e..8206e32 100755 --- a/R/BuidTree.R +++ b/R/BuidTree.R @@ -525,10 +525,12 @@ setMethod(f="AddTree", #' @import reshape2 setMethod(f="Add_DepthMatrix", signature="redeemR", - definition=function(object){ + definition=function(object,QualifiedTotalCts=""){ require(reshape2) message("Remember to update for combined object") + if(length(QualifiedTotalCts)==0){ QualifiedTotalCts<-read.table(paste(object@attr$path,"/QualifiedTotalCts",sep="")) + } colnames(QualifiedTotalCts)<-c("Cell","Pos","T","LS","S","VS") Dic<-gsub("Variants","",colnames(object@Cts.Mtx.bi)) %>% substr(.,1,nchar(.)-2) %>% as.integer %>% data.frame(Variants=colnames(object@Cts.Mtx.bi),Pos=.) QualifiedTotalCts.subset<-subset(QualifiedTotalCts,Cell %in% row.names(object@Cts.Mtx.bi)) %>% merge(.,Dic,by="Pos") %>% .[,c("Cell","Variants",object@para["Threhold"])] diff --git a/man/Add_DepthMatrix-redeemR-method.Rd b/man/Add_DepthMatrix-redeemR-method.Rd index a6c5522..bc161a9 100644 --- a/man/Add_DepthMatrix-redeemR-method.Rd +++ b/man/Add_DepthMatrix-redeemR-method.Rd @@ -5,7 +5,7 @@ \title{Add_DepthMatrix Optional, add a matrix with same dimension with the Cts.Mtx and Cts.Mtx.bi, which display the depths} \usage{ -\S4method{Add_DepthMatrix}{redeemR}(object) +\S4method{Add_DepthMatrix}{redeemR}(object, QualifiedTotalCts = "") } \arguments{ \item{object}{redeemR class}