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thierrygosselin avatar thierrygosselin commented on June 5, 2024

Hi Rita,
I'll have a look at your problem today
Thanks for reporting.
Thierry

from radiator.

thierrygosselin avatar thierrygosselin commented on June 5, 2024

Hi Rita,

try updating radiator and try 2 tests with the files you provided:

  1. 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
  1. 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.

rcastil avatar rcastil commented on June 5, 2024

Dear Thierry,
No problems now!
Many thanks,
R

from radiator.

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