[R] question about system.file()

[Duncan Murdoch]

On 10/04/2020 3:46 p.m., Ana Marija 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

Just use "output4.bed" as the filename.  The system.file() function is 
for working out the filename of files installed in packages.

Duncan Murdoch

> 
> 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
> 
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