Comments (3)
Hi Rita,
I'll have a look at your problem today
Thanks for reporting.
Thierry
from radiator.
Hi Rita,
try updating radiator and try 2 tests with the files you provided:
- test1
test1 <- radiator::filter_hwe(data = radiator.gen, interactive.filter = TRUE)
This is the interactive version, you will have to enter things
- y
- 4
- try 3 but you likely have to use 2 or 1 (it will ask until it found a dataset with the values)
For the function documentation:
?radiator::filter_hwe
These are the files and folders generated:
blacklist.markers.hwd.0.001.mid.p.value.4.hw.pop.threshold.tsv
blacklist.markers.hwd.0.05.mid.p.value.4.hw.pop.threshold.tsv
[email protected]
genotypes.summary.tsv
hw.pop.sum.tsv
hwd.helper.table.tsv
hwd.plot.blacklist.markers.pdf
hwe.manhattan.plot.pdf
hwe.ternary.plots.missing.data.pdf
[email protected]
tidy.filtered.hwe.0.001.mid.p.value.4.hw.pop.threshold.rad
tidy.filtered.hwe.0.05.mid.p.value.4.hw.pop.threshold.rad
whitelist.markers.hwe.0.001.mid.p.value.4.hw.pop.threshold.tsv
whitelist.markers.hwe.0.05.mid.p.value.4.hw.pop.threshold.tsv
- test2 (no interaction)
test2 <- radiator::filter_hwe(data = radiator.gen, interactive.filter = FALSE, hw.pop.threshold = 4, midp.threshold = 1)
These are the files and folders generated:
blacklist.markers.hwd.0.001.mid.p.value.4.hw.pop.threshold.tsv
blacklist.markers.hwd.0.05.mid.p.value.4.hw.pop.threshold.tsv
[email protected]
genotypes.summary.tsv
hw.pop.sum.tsv
hwd.helper.table.tsv
hwd.plot.blacklist.markers.pdf
hwe.manhattan.plot.pdf
hwe.ternary.plots.missing.data.pdf
[email protected]
tidy.filtered.hwe.0.001.mid.p.value.4.hw.pop.threshold.rad
tidy.filtered.hwe.0.05.mid.p.value.4.hw.pop.threshold.rad
whitelist.markers.hwe.0.001.mid.p.value.4.hw.pop.threshold.tsv
whitelist.markers.hwe.0.05.mid.p.value.4.hw.pop.threshold.tsv
Please re-open the issue if your still experiencing problems
Thierry
from radiator.
Dear Thierry,
No problems now!
Many thanks,
R
from radiator.
Related Issues (20)
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- Genomic converter error 'no more individuals in your data' HOT 9
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- Error when using genomic_converter genlight --> pcadapt HOT 3
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- genomic converter() Error:>! `everything()` must be used within a *selecting* function. HOT 1
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from radiator.