| getTrueModel {simulatorZ} | R Documentation |
The parametric bootstrap simulation depends on the true model of original sets. This function is to generate useful values from the true models for further analysis. We fit CoxBoost to the original sets and use the coefficients to simulate the survival and censoring time. grid, survH, censH, which are useful for this purpose. grid=grid corresponding to hazard estimations censH and survH survH=cumulative hazard for survival times distribution censH=cumulative hazard for censoring times distribution
getTrueModel(obj, y.vars, parstep)
obj |
a list of ExpressionSets, matrix or RangedSummarizedExperiment |
y.vars |
a list of response variables, Surv, matrix or data.frame object |
parstep |
number of steps in CoxBoost |
returns a list of values: beta: True coefficients obtained by fitting CoxBoost to the original ExpressionSets grid: timeline grid corresponding to hazard estimations censH and survH survH: cumulative hazard for survival times distribution censH: cumulative hazard for censoring times distribution lp: true linear predictors
Yuqing Zhang, Christoph Bernau, Levi Waldron
library(curatedOvarianData)
data(GSE17260_eset)
data(E.MTAB.386_eset)
data(GSE14764_eset)
esets <- list(GSE17260=GSE17260_eset, E.MTAB.386=E.MTAB.386_eset, GSE14764=GSE14764_eset)
esets.list <- lapply(esets, function(eset){
return(eset[1:500, 1:20])
})
## simulate on multiple ExpressionSets
set.seed(8)
y.list <- lapply(esets.list, function(eset){
time <- eset$days_to_death
cens.chr <- eset$vital_status
cens <- c()
for(i in seq_along(cens.chr)){
if(cens.chr[i] == "living") cens[i] <- 1
else cens[i] <- 0
}
y <- Surv(time, cens)
return(y)
})
res1 <- getTrueModel(esets.list, y.list, 100)
## Get true model from one set
res2 <- getTrueModel(esets.list[1], y.list[1], 100)
names(res2)
res2$lp
## note that y.list[1] cannot be replaced by y.list[[1]]