deconv <- function(b, stat, nb.arch.grid) {
### Weights
pathArch <- Arguments$getWritablePath(sprintf("archetypeData%s_%s_c3co", stat, framework))
pathc3co <- Arguments$getWritablePath(sprintf("%s/features_B=%s/", pathArch, b))
filename <- sprintf("archData_B=%s_%s.rds", b, "c3co")
filepath <- file.path(pathc3co,filename)
if (!file.exists(filepath)|| forcec3co){
dat <- readRDS(sprintf("%s/dat_B=%s.rds", pathSim, bb))
casRes <- c3co(dat, nb.arch.grid=nb.arch.grid, stat=stat, output.dir=pathc3co)
saveRDS(casRes, filepath)
}
}
dummy <- mclapply(B, deconv, stat="C1C2", nb.arch.grid=p.list, mc.cores = mc.cores)
dummy <- mclapply(B, deconv, stat="TCN", nb.arch.grid=p.list, mc.cores = mc.cores)
pathArch <- Arguments$getWritablePath(sprintf("archetypeData%s_%s_FLLAT", "TCN", framework))
deconvFLLAT <- function(b) {
### Weights
pathSim <- Arguments$getWritablePath("simData")
dat <- readRDS(sprintf("%s/dat_B=%s.rds", pathSim, b))
YTCNtoSeg <- t(sapply(dat, function(cc) cc$tcn))
Y <- log2(YTCNtoSeg)-1
pathfllat <- Arguments$getWritablePath(sprintf("%s/features_B=%s/", pathArch, b))
filename <- sprintf("archData_B=%s_%s.rds", b, "FLLAT")
filepath <- file.path(pathfllat,filename)
if(!file.exists(filepath)|| force){
result.pve <- FLLat.PVE(na.omit(t(Y)),J.seq=p.list)
result.FLLAT <- sapply(p.list, function(pp) {
rr <- FLLat.BIC(na.omit(t(Y)),J=pp)
W <- rr$opt.FLLat$Theta
Z <- rr$opt.FLLat$Beta
resFLLAT <- list(res=list(Z=Z, W=t(W),Y.hat=(Y=t(W)%*%t(Z))), PVE=result.pve[which(pp==p.list)])
saveRDS(resFLLAT,sprintf("%s/featureData,p=%s.rds",pathfllat,pp))
})
saveRDS(result.FLLAT, filepath)
}else{
print("file already exists")
}
}
dummy <- mclapply(B, deconvFLLAT, mc.cores = mc.cores)
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