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Changed res_ai[1] to res_ai[,1] to obtain the correct telomeric AI #2

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Changed res_ai[1] to res_ai[,1] to obtain the correct telomeric AI #2

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ca54048
Changed res_ai[1] to res_ai[,1] to obtain the correct telomeric alle…
mxdeluca Sep 2, 2018
9f96797
wrong index for nA
mxdeluca Nov 9, 2018
17b67dd
wrong index nA
mxdeluca Nov 9, 2018
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3 changes: 1 addition & 2 deletions R/calc.hrd.R
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
#' @param nA column number of copy number of A allele
#' @param sizelimit lower limit of the size of LOHs
#' @return number of LOH
calc.hrd<-function(seg, nA=7, return.loc=FALSE,sizelimit1){
calc.hrd<-function(seg, nA=6, return.loc=FALSE,sizelimit1){
nB <- nA+1
output <- rep(0, length(unique(seg[,1])))
names(output) <- unique(seg[,1])
Expand Down Expand Up @@ -40,4 +40,3 @@ calc.hrd<-function(seg, nA=7, return.loc=FALSE,sizelimit1){
return(output)
}
}

2 changes: 1 addition & 1 deletion R/calc.lst.R
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Expand Up @@ -5,7 +5,7 @@
#' @param nA column number of copy number of A allele
#' @param chr.arm option to use chromosome arms defined during segmentation
#' @return number of LSTs
calc.lst<-function(seg, chrominfo=chrominfo,nA=7,chr.arm='no'){
calc.lst<-function(seg, chrominfo=chrominfo,nA=6,chr.arm='no'){
nB <- nA+1
samples <- unique(seg[,1])
output <- setNames(rep(0,length(samples)), samples)
Expand Down
14 changes: 7 additions & 7 deletions R/scar_score.R
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Expand Up @@ -43,19 +43,19 @@ scar_score<-function(seg,reference = "grch38", seqz=FALSE, ploidy=NULL, sizelimi
res_ai<- calc.ai_new(seg = seg, chrominfo = chrominfo) #<-- the first column is what I need
#Calculating the large scale transition scores:
res_lst <- calc.lst(seg = seg, chrominfo = chrominfo) #<-- You need to use the chrominfo.snp6 file! Nicolai sent it to you!
sum_HRD0<-res_lst+res_hrd+res_ai[1]
sum_HRD0<-res_lst+res_hrd+res_ai[,1]

if (is.null(ploidy)){
sum_HRDc<-NA
} else {
sum_HRDc<-res_lst-15.5*ploidy+res_hrd+res_ai[1]
sum_HRDc<-res_lst-15.5*ploidy+res_hrd+res_ai[,1]
}

#HRDresulst<-c(res_hrd,res_ai,res_lst,sum_HRD0,sum_HRDc)
#HRDresulst<-cbind(res_hrd,res_ai[,1],res_lst,sum_HRD0,sum_HRDc)
#names(HRDresulst)<-c("HRD",colnames(res_ai),"LST", "HRD-sum","adjusted-HRDsum")
HRDresulst<-c(res_hrd,res_ai[1],res_lst,sum_HRD0)
names(HRDresulst)<-c("HRD",colnames(res_ai)[1],"LST", "HRD-sum")
run_name<-names(sum_HRD0)
write.table(t(HRDresulst),paste0(outputdir,"/",run_name,"_HRDresults.txt"),col.names=NA,sep="\t",row.names=unique(seg[,1]))
HRDresulst<-cbind(res_hrd,res_ai[,1],res_lst,sum_HRD0)
colnames(HRDresulst)<-c("HRD",colnames(res_ai)[1],"LST", "HRD-sum")
assign("HRDresulst",as.data.frame(HRDresulst),envir = .GlobalEnv)
write.table(t(HRDresulst),paste0(outputdir,"/","HRDresults.txt"),sep="\t")
return(t(HRDresulst))
}