I believe you have to wrap objects in the I() function to stop DataFrame trying to coerce your parameters to a DataFrame
> y <- as(c(1,0,1,0,1,0),"sparseVector") > a = DataFrame(spvec = I( y ) ) > a[,1] sparse vector (nnz/length = 3/6) of class "dsparseVector" [1] 1 . 1 . 1 . However, you can't display the variable 'a', as it again tries to coerce it and fails: > a DataFrame with 6 rows and 1 column Error in as.matrix(format(as.data.frame(lapply(object, showAsCell), optional = TRUE))) : error in evaluating the argument 'x' in selecting a method for function 'as.matrix': Error in as.data.frame.default(x[[i]], optional = TRUE) : cannot coerce class '"dsparseVector"' into a data.frame Tim On 22/01/2013 10:02, "Michael Love" <l...@molgen.mpg.de> wrote: >hi all, > >I am having trouble putting sparse vectors as columns of a DataFrame. >They have 'length' and '[' methods: > > > library(Matrix) > > library(IRanges) > > y <- as(c(1,0,1,0,1,0),"sparseVector") > > y >sparse vector (nnz/length = 3/6) of class "dsparseVector" >[1] 1 . 1 . 1 . > > y[6] >sparse vector (nnz/length = 0/1) of class "dsparseVector" >[1] . > > length(y) >[1] 6 > > DataFrame(spvec = y) >Error in DataFrame(spvec = y) : > cannot coerce class "dsparseVector" to a DataFrame > > > sessionInfo() >R Under development (unstable) (2012-10-31 r61057) >Platform: x86_64-unknown-linux-gnu (64-bit) > >locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C >[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > >attached base packages: >[1] parallel stats graphics grDevices utils datasets methods >[8] base > >other attached packages: >[1] IRanges_1.17.26 BiocGenerics_0.5.6 Matrix_1.0-10 >[4] lattice_0.20-13 Defaults_1.1-1 BiocInstaller_1.9.6 > >loaded via a namespace (and not attached): >[1] grid_2.16.0 stats4_2.16.0 tools_2.16.0 > > >thanks! > >Mike > >_______________________________________________ >Bioc-devel@r-project.org mailing list >https://stat.ethz.ch/mailman/listinfo/bioc-devel ________________________________ This email is confidential and intended solely for the u...{{dropped:12}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
