Nothing
## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
library(mets)
## -----------------------------------------------------------------------------
types <- c("DCGCGCTCACG","DTCCGCTGACG","ITCAGTTGACG","ITCCGCTGAGG")
## some haplotypes frequencies for simulations
data(hapfreqs)
print(hapfreqs)
## -----------------------------------------------------------------------------
www <-which(hapfreqs$haplotype %in% types)
hapfreqs$freq[www]
baseline=hapfreqs$haplotype[9]
baseline
## -----------------------------------------------------------------------------
data(haploX)
dlist(haploX,.~id|id %in% c(1,4,7))
## -----------------------------------------------------------------------------
data(hHaplos) ## loads ghaplos
head(ghaplos)
## -----------------------------------------------------------------------------
designftypes <- function(x,sm=0) {
hap1=x[1]
hap2=x[2]
if (sm==0) y <- 1*( (hap1==types) | (hap2==types))
if (sm==1) y <- 1*(hap1==types) + 1*(hap2==types)
return(y)
}
## -----------------------------------------------------------------------------
haploX$time <- haploX$times
Xdes <- model.matrix(~factor(time),haploX)
colnames(Xdes) <- paste("X",1:ncol(Xdes),sep="")
X <- dkeep(haploX,~id+y+time)
X <- cbind(X,Xdes)
Haplos <- dkeep(ghaplos,~id+"haplo*"+p)
desnames=paste("X",1:6,sep="") # six X's related to 6 cycles
head(X)
## -----------------------------------------------------------------------------
out <- haplo.surv.discrete(X=X,y="y",time.name="time",
Haplos=Haplos,desnames=desnames,designfunc=designftypes)
names(out$coef) <- c(desnames,types)
out$coef
summary(out)
## -----------------------------------------------------------------------------
tcoef=c(-1.93110204,-0.47531630,-0.04118204,-1.57872602,-0.22176426,-0.13836416,
0.88830288,0.60756224,0.39802821,0.32706859)
cbind(out$coef,tcoef)
## -----------------------------------------------------------------------------
head(out$X,10)
## -----------------------------------------------------------------------------
sessionInfo()
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