Comments (9)
thierrygosselin
commented on June 16, 2024
Hi Erica,
It's likely a problem of individual naming inside the plink or the strata file, but I won't know for sure until I have the data to run the function and reproduce the error. You mind sharing relevant files over email ?
Best
Thierry
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esnielsen
commented on June 16, 2024
Hi Thierry,
Thanks so much for the quick reply!
The strata file is attached, and here’s a link to the .bed file: https://www.dropbox.com/s/ws87l798ka9vreg/ALL_2.bin.bed?dl=0 <https://www.dropbox.com/s/ws87l798ka9vreg/ALL_2.bin.bed?dl=0>
Thanks,
Erica
… On 17 Nov 2022, at 15:51, Thierry Gosselin ***@***.***> wrote:
Hi Erica,
It's likely a problem of individual naming inside the plink or the strata file, but I won't know for sure until I have the data to run the function and reproduce the error. You mind sharing relevant files over email ?
Best
Thierry
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thierrygosselin
commented on June 16, 2024
I don't see the strata file
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thierrygosselin
commented on June 16, 2024
Do you have the corresponding fam and bim files that goes with the bed file ?
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esnielsen
commented on June 16, 2024
Hi, yes all the files should be here: https://www.dropbox.com/scl/fo/dmh7l3ewfyr3wmvn1t78w/h?dl=0&rlkey=n913sdaqiskp57ahm0ivxjow6 <https://www.dropbox.com/scl/fo/dmh7l3ewfyr3wmvn1t78w/h?dl=0&rlkey=n913sdaqiskp57ahm0ivxjow6>
… On 17 Nov 2022, at 17:35, Thierry Gosselin ***@***.***> wrote:
Do you have the corresponding fam and bim files that goes with the bed file ?
—
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thierrygosselin
commented on June 16, 2024
ok good I have what I need
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thierrygosselin
commented on June 16, 2024
I was able to reproduce the bug, will have a fix this afternoon
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esnielsen
commented on June 16, 2024
Great, thanks so much!
… On 17 Nov 2022, at 18:12, Thierry Gosselin ***@***.***> wrote:
I was able to reproduce the bug, will have a fix this afternoon
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thierrygosselin
commented on June 16, 2024
Found the problem
I don't know the origin of this plink file (how it was generated), but the names inside the bed and fam files don't match. Or it's SeqArray::seqBED2GDS use under the hood that's not working.
Same goes with the strata file which is completely different than the fam file naming scheme.
Some advice on naming strategy, here, but it doesn't have to be that way to work inside radiator.
once this is sorted out try:
test1 <- radiator::read_plink(data = "ALL_2.bin.bed")
if it's not working, don't bother trying genomic_converter,
re-open the issue if you're still having problems
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