gl2vcf question

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Alice Atikessé

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Dec 31, 2022, 10:44:43 AM12/31/22
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Hello Luis and DartR team!

I have a very basic question here: 
What is meant to go in the "plink_path" line of the gl2vcf() function? It says "Path of PLINK binary file [default getwd())]." but I am not sure about the meaning of that. Do I have to already have a PLINK file somewhere or is it a outpath directory? I'm douting since there's already an outpath line in the function...

gl2vcf( x, plink_path = getwd(), outfile = "gl_vcf", outpath = tempdir(), snp_pos = "0", snp_chr = "0", chr_format = "character", pos_cM = "0", ID_dad = "0", ID_mom = "0", sex_code = "unknown", phen_value = "0", verbose = NULL )

Thank you very much for your help,
Happy New Year!

Alice 

Berry, Olly (NCMI, IOMRC Crawley)

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Dec 31, 2022, 8:58:08 PM12/31/22
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Hi Alice and happy new year!
I *think I can help. To run this function, you need to have downloaded the Plink binary file and the part of the script you refer to is where you specify where you have saved the plink binary to. See here: https://search.r-project.org/CRAN/refmans/dartR/html/gl2vcf.html.
The default is to look in your working directory, but you can save it elsewhere if you provide the appropriate path.
Hope that helps.
Cheers,
Olly
Olly Berry
Director, CSIRO Environomics Future Science Platform


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Alice Atikessé

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Jan 1, 2023, 11:35:31 AM1/1/23
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Hi Olly,
Thank you for your quick answer!
This bring me to another question: how do you download the PLINK binary file in the first place since my initial file is a dart file? I suppose it's with the gl2plink() function but there's also the same "plink_path" line there. 

Thanks again!

Alice

Berry, Olly (NCMI, IOMRC Crawley)

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Jan 1, 2023, 5:28:05 PM1/1/23
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Hi Alice,
If you look at the details section of the function description, there is a link to where you can download the plink program.

Details

This function requires to download the binary file of PLINK 1.9 and provide its path (plink_path). The binary file can be downloaded from: https://www.cog-genomics.org/plink/

Is this what you mean?

Cheers,

Olly 

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Sent: Monday, January 2, 2023 12:35:31 AM
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Subject: Re: [dartR] gl2vcf question
 

Alice Atikessé

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Jan 1, 2023, 5:49:06 PM1/1/23
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Hi Olly,
So if my initial goal is to convert my dart file in a vcf file, I have no choice but to download PLINK on my computer in the first place (if I understand correctly). The meaning of the term "binary file" is simply the way the PLINK program is called right? Because I was confusing this term with my genomic file (my own data). 

Thank you so much, I think I get it now!

Alice

Berry, Olly (NCMI, IOMRC Crawley)

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Jan 1, 2023, 9:19:23 PM1/1/23
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I think you’re in the right track now Alice. Good luck :-)

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Sent: Monday, January 2, 2023 6:49:06 AM
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