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family information in snpgdsGDS2PED #70

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treebreeder opened this issue Sep 2, 2020 · 2 comments
Open

family information in snpgdsGDS2PED #70

treebreeder opened this issue Sep 2, 2020 · 2 comments

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@treebreeder
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How can I translate my .gds into .ped and automatically taking the family information from my gds object which I added before with add.gdsn() ?

Such as from:

  • [ ]
    |--+ sample.id { Str8 173 LZMA_ra(15.7%), 577B }
    |--+ snp.id { Int32 17489 LZMA_ra(16.9%), 11.5K }
    |--+ snp.position { Int32 17489 LZMA_ra(58.1%), 39.7K }
    |--+ snp.chromosome { UInt8 17489 LZMA_ra(37.7%), 6.4K }
    |--+ snp.allele { Str8 17489 LZMA_ra(12.9%), 8.8K }
    |--+ snp.rs.id { Str8 17489 LZMA_ra(0.77%), 141B }
    |--+ genotype { Bit2 173x17489, 738.7K } *
    |--+ pop_code { Int32,factor 173, 692B } *
    --+ fam [ data.frame ] *
    --+ pop { Int32,factor 173, 692B } *
@zhengxwen
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snpgdsGDS2PED() and snpgdsGDS2BED() do not have such function.
But I could consider adding the function in future.

@treebreeder
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I think this would be nice, since it would save some extra work when you have to manipulate the ped file afterwards, although the necessary information is potentially already there!
Thanks

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