[Bioc-devel] sparse vectors as DataFrame columns

[Tim Yates]

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" <love at 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
>
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