Thanks very much Dimitrius and David. I want to compute CPE using pre-calculated beta-model and linear.predictor using the following code. I hope it the code is OK. Let me know. I am also doing some sanity checks.
testc$x <- scores testc$y <- Surv(testdata$time,testdata$status) testfit <- coxph(y ~ x, testc, iter.max=0, init=1) cpe=phcpe(testfit) Thanks very much again. ----- On Sun, Mar 13, 2011 at 2:28 PM, David Winsemius <dwinsem...@comcast.net>wrote: > > On Mar 13, 2011, at 1:32 PM, Dimitris Rizopoulos wrote: > > probably you want to use the 'init' argument and 'iter.max' >> control-argument of coxph(). For example, for the Lung dataset, we fix the >> coefficients of age and ph.karno at 0.05 and -0.05, respectively: >> >> library(survival) >> >> coxph(Surv(time, status) ~ age + ph.karno, data = lung, >> init = c(0.05, -0.05), iter.max = 0) >> > > >> >> I hope it helps. >> >> Best, >> Dimitris >> >> >> On 3/13/2011 6:08 PM, Angel Russo wrote: >> >>> I need to force a coxph() function in R to use a pre-calculated set of >>> beta >>> coefficients of a gene signature consisting of xx genes and the gene >>> expression is also provided of those xx genes. >>> >> > I would have guessed (and that is all one can do without an example and > better description of what the setting and goal might be) that the use of > the offset capablity in coxph might be needed. > > -- > David. > > >>> If I try to use "coxph()" function in R using just the gene expression >>> data >>> alone, the beta coefficients and coxph$linear.predictors will change and >>> I >>> need to use the pre-calcuated linear predictor not re-computed using >>> coxph() >>> function. The reason is I need to compute a quantity that uses as it's >>> input >>> the coxph() output but I need this output to be pre-calculated >>> beta-coefficients and linear.predictor. >>> >>> Any one can show me how to do this in R? >>> >>> Thanks a lot. >>> >> > David Winsemius, MD > West Hartford, CT > > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.