Nothing
### Computing time experiences
pp <- 100
len <- 10^4
onlySNP=FALSE
source('R/00.setup.R')
source('R/01.createDataSets.R')
source("R/02e.PSCBS.R")
source("R/02a.RBS+DP.R")
source("R/02c.cghseg.R")
source("R/02d.CBS.R")
source("R/02f.GFLars.R")
source("R/02g.CnaStruct.R")
source("R/02i.DPSeg2d.R")
## Run only with version 2.15 ofR
if(version$major<3){source("R/02b.PSCN.R")}
methTags <- c(sprintf("DP:c (Kmax=%s)", candK),
sprintf("CnaStruct (Kmax=%s)", candK),
sprintf("DPseg:log(c),d (Kmax=%s)", candK),
"CBS:log(c)",
"PSCBS",
sprintf("RBS+DP:log(c),d (Kmax=%s)", candK),
sprintf("GFLars+DP:log(c) (Kmax=%s)", candK),
sprintf("GFLars+DP:log(c),d (Kmax=%s)", candK),
"PSCN"
)
source('R/00.setup.R')
times <- as.matrix(sapply(methTags, function(methTag){
print(methTag)
tt <- sapply(1:B, function(bb){
filename <- sprintf("%s,b=%s,%s.xdr", simNameNF, bb, methTag)
pathname <- file.path(tpath, filename)
if(file.exists(pathname)){
if(methTag%in%c("DP:c (Kmax=50)","DPseg:log(c),d|het (Kmax=50)","CnaStruct (Kmax=50)")){
time <- loadObject(pathname)
}else{
time <- loadObject(pathname)["segmentation"]
}
return(time)
}else{
return(NA)
}
})
return(mean(tt,na.rm=TRUE))
}), ncol = 1)
library(xtable)
rownames(times) <- gsub("\\+DP","",gsub("\\(Kmax=(.*)\\)","",gsub(".segmentation", "", rownames(times))))
colnames(times) <- sprintf("Time(n = %s)", len)
xtable(times)
pp <- 100
len <- 10^5
onlySNP=FALSE
source('R/00.setup.R')
source('R/01.createDataSets.R')
source("R/02e.PSCBS.R")
source("R/02a.RBS+DP.R")
source("R/02c.cghseg.R")
source("R/02d.CBS.R")
source("R/02f.GFLars.R")
## Run only with version 2.15 of R
if(version$major<3){source("R/02b.PSCN.R")}
methTags <- c(sprintf("DP:c (Kmax=%s)", candK),
sprintf("CnaStruct (Kmax=%s)", candK),
sprintf("DPseg:log(c),d (Kmax=%s)", candK),
"CBS:log(c)",
"PSCBS",
sprintf("RBS+DP:log(c),d (Kmax=%s)", candK),
sprintf("GFLars+DP:log(c) (Kmax=%s)", candK),
sprintf("GFLars+DP:log(c),d (Kmax=%s)", candK),
"PSCN"
)
B=10
times2 <- as.matrix(sapply(methTags, function(methTag){
print(methTag)
tt <- sapply(1:B,function(bb){
filename <- sprintf("%s,b=%s,%s.xdr", simNameNF, bb, methTag)
pathname <- file.path(tpath, filename)
if(file.exists(pathname)){
if(methTag%in%c("DP:c (Kmax=50)","DPseg:log(c),d|het (Kmax=50)","CnaStruct (Kmax=50)")){
time <- loadObject(pathname)
}else{
time <- loadObject(pathname)["segmentation"]
}
}else{time <- NA}
time
})
return(mean(tt, na.rm=TRUE))
}), ncol = 1)
library(xtable)
rownames(times2) <- gsub("\\+DP","",gsub("\\(Kmax=(.*)\\)","",gsub(".segmentation", "", rownames(times))))
colnames(times2) <- sprintf("Time(n = %s)", len)
xtable(times2)
xtable(cbind(times,times2))
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