tail() is broken for Surv objects, because despite Surv objects exposing their implementation as matrices (probably a bad decision), they do not inherit from class "matrix". One option is to make length.Surv return the number of elements (rows in the matrix) instead of the number of cells, but who knows how much code that would break. I filed an issue on their GitHub project: https://github.com/therneau/survival/issues/22
Michael On Sun, May 28, 2017 at 5:20 PM, Levi Waldron <lwaldron.resea...@gmail.com> wrote: > Running and updated Bioc 3.5: > > > library(survival) > > set.seed(1) > > cens <- sample(0:1, 100, replace=TRUE) > > time <- rnorm(100) > > df = DataFrame(time=time, cens=cens, y=Surv(time, cens)) > > df[1:3, ] #OK > DataFrame with 3 rows and 3 columns > time cens y.from > <numeric> <integer> <Surv> > 1 0.3981059 0 0.398105880367068:0 > 2 -0.6120264 0 -0.612026393250771:0 > 3 0.3411197 1 0.341119691424425:1 > > df #error > DataFrame with 100 rows and 3 columns > *Error in unclass(x)[i, , drop = FALSE] : subscript out of bounds* > > > > This came up after I noticed something similar in > MultiAssayExperiment::wideFormat() when trying to reshape a Surv column, > but I'm not sure it's a bug in MultiAssayExperiment: > > > library(MultiAssayExperiment) > > miniACC$y <- Surv(miniACC$days_to_death, miniACC$vital_status) > > res = wideFormat(miniACC["EZH2", , ], colDataCols="y") > Show Traceback > > Rerun with Debug > * Error in unclass(x)[i, , drop = FALSE] : subscript out of bounds * > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
