[R] question about system.file()

[Ana Marija]

I tried to do this but I got this error:

> bed.fn <- system.file("output4.bed", package="SNPRelate")
> dim(bed.fn)
NULL
> fam.fn <- system.file("output4.fam", package="SNPRelate")
> bim.fn <- system.file("output4.bim", package="SNPRelate")
> snpgdsBED2GDS(bed.fn, fam.fn, bim.fn, "HapMap.gds")
Start file conversion from PLINK BED to SNP GDS ...
Error in (function (con, what, n = 1L, size = NA_integer_, signed = TRUE,  :
  can only read from a binary connection
In addition: Warning message:
In file(filename, "rb") :
  file("") only supports open = "w+" and open = "w+b": using the former

On Fri, Apr 10, 2020 at 2:46 PM Ana Marija <sokovic.anamarija using gmail.com> wrote:
>
> Hello,
>
> I would like to try this example in this link:
> https://www.rdocumentation.org/packages/SNPRelate/versions/1.6.4/topics/snpgdsBED2GDS
>
> for example this line:
>
> bed.fn <- system.file("extdata", "plinkhapmap.bed.gz", package="SNPRelate")
>
> I have in current directory from where I would run this function a
> file named output4.bed
>
> in order to run the above, can I just run this:
> bed.fn <- system.file("output4.bed", package="SNPRelate")
>
> what is "extdata" ? Do I need it if my output4.bed is in the directory
> from where I am running this?
>
> Also do I need to have .gz format of output4.bed?
>
> Thanks
> Ana