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question about system.file()

8 messages · Ana Marija, Duncan Murdoch, Rasmus Liland +3 more

Original
Ana Marija
# 
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
Ana Marija
# 
I tried to do this but I got this error:
NULL
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 at gmail.com> wrote:
Duncan Murdoch
#
On 10/04/2020 3:46 p.m., Ana Marija wrote:
Just use "output4.bed" as the filename.  The system.file() function is 
for working out the filename of files installed in packages.

Duncan Murdoch
Ana Marija
# 
Got it, thanks!
On Fri, Apr 10, 2020 at 2:54 PM Duncan Murdoch <murdoch.duncan at gmail.com> wrote:
Rasmus Liland
#
On Fri, Apr 10, 2020 at 2:54 PM Duncan Murdoch wrote:
"extdata" is a directory of five example 
files from the SNPRelate package: 
hapmap_geno.gds, plinkhapmap.bed.gz, 
plinkhapmap.bim.gz, plinkhapmap.fam.gz, 
and sequence.vcf.  On my system the 
directory is in 
~/R/x86_64-pc-linux-gnu-library/3.6/SNPRelate/extdata 
...
Not if the files were not gzipped, you 
do not.  Example files in packages are 
compressed to save space for example 
code you will maybe will try only once, 
four of the files in that directory are 
gzipped, I do not know about that vCard 
file ...  Just input your own paths.

Try to find your files using 
list.files(".", "bed$") or something 
...
On 2020-04-10 14:49 -0500, Ana Marija wrote:
Thus, try this:

  bed.fn <- "output4.bed"
  fam.fn <- "output4.fam"
  bim.fn <- "output4.bim"
  SNPRelate::snpgdsBED2GDS(bed.fn, fam.fn, bim.fn, "output4.gds")

Best,
Rasmus
Anand Menon
# 
Hello, Could you please help unsubscribe me from these emails. Thank you.

Kind Regards,
Anand K Menon
Cell: 1-416-939-3671


On Fri, Apr 10, 2020 at 3:46 PM Ana Marija <sokovic.anamarija at gmail.com>
wrote:

  
  


  


      

    

    

      
      

        


  

        

      Rui Barradas
    

    

      
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Hello,

There are instructions to unsubscribe at the bottom of this e-mail and 
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Hope this helps,

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?s 04:33 de 11/04/20, Anand Menon escreveu:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Jeff Newmiller
    

    

      
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On April 10, 2020 8:33:41 PM PDT, Anand Menon <anandmenon.12 at gmail.com> wrote: