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voichek / kmersGWAS

A library for running k-mers based GWAS
GNU General Public License v3.0
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making binary 0/1 PAV table usable in r #122

Closed renhamm closed 2 years ago

renhamm commented 2 years ago

I am using the first half of this method (up to when the PAV table has been generated), and then redirecting the PAV table to be used for GEA analysis. I have successfully generated the NAME_table.table binary file, but am having a difficult time converting this to a usable flatfile format to upload as a dataframe into R without knowing the number of columns and rows. I'm assuming the columns are the individual names in the order they appear in the later generated .fam file, but I have no idea how to determine how many rows (kmers?) to include.

Is there a suggested method for converting the binary table file into a usable dataframe?

voichek commented 2 years ago

Dear Ren,

To convert it from my binary formatting to textual format I suggest going through the PLINK binary file and then converting to VCF.

Best, Yoav

renhamm commented 2 years ago

That worked! Thank you.