DrK-Lo
commented
1 year ago Can you check your code? It looks like in your first two lines of code, the right trim fraction is changed from 0.05 to 0.5
From: dmacguigan @.> Sent: 01 March 2023 17:16 To: whitlock/OutFLANK @.> Cc: Subscribed @.***> Subject: [whitlock/OutFLANK] Different RightTrimFraction settings give same p values (Issue #32)
If I understand correctly, modifying the RightTrimFraction or LeftTrimFraction parameters of the OutFLANK function changes the Fst values used to estimate the Fst distribution. Since the Fst distribution is different, we should expect different p-values.
When I change the LeftTrimFraction parameter, the right-tailed p-values are different.
outflank_results_1 <- OutFLANK(FstDataFrame = outflank_dat, LeftTrimFraction=0.05, RightTrimFraction=0.05, Hmin=0.1, NumberOfSamples=2, qthreshold=0.05)
outflank_results_2 <- OutFLANK(FstDataFrame = outflank_dat, LeftTrimFraction=0.05, RightTrimFraction=0.5, Hmin=0.1, NumberOfSamples=2, qthreshold=0.05)
plot(outflank_results_1$results$pvaluesRightTail,outflank_results_2$results$pvaluesRightTail) abline(0,1, col="red", lwd=2)
However, when I change the RightTrimFraction parameter, the resulting p-values are identical.
outflank_results_1 <- OutFLANK(FstDataFrame = outflank_dat, LeftTrimFraction=0.05, RightTrimFraction=0.05, Hmin=0.1, NumberOfSamples=2, qthreshold=0.05)
outflank_results_2 <- OutFLANK(FstDataFrame = outflank_dat, LeftTrimFraction=0.05, RightTrimFraction=0.75, Hmin=0.1, NumberOfSamples=2, qthreshold=0.05)
plot(outflank_results_1$results$pvaluesRightTail,outflank_results_2$results$pvaluesRightTail) abline(0,1, col="red", lwd=2)
I have attached my data (outflank_dat) if you would like to try replicating these results. outflank_dat.txthttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fwhitlock%2FOutFLANK%2Ffiles%2F10865685%2Foutflank_dat.txt&data=05%7C01%7Ck.lotterhos%40northeastern.edu%7C88e974ae8a6641a19e1908db1aa2a8de%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C638133058146994196%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=1noIjBv4QyR7oMBp85tJy3eOhMcOwycmROsmyQVPl3s%3D&reserved=0
Do you have any thoughts on why this is happening? I would like to adjust my RightTrimFraction parameter because I suspect there are many loci under selection in my dataset. But at the moment, adjusting that parameter has no effect.
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dmacguigan
If I understand correctly, modifying the
RightTrimFractionorLeftTrimFractionparameters of theOutFLANKfunction changes the Fst values used to estimate the Fst distribution. Since the Fst distribution is different, we should expect different p-values.When I change the
LeftTrimFractionparameter, the right-tailed p-values are different.However, when I change the
RightTrimFractionparameter, the resulting p-values are identical.I have attached my data (outflank_dat) if you would like to try replicating these results. outflank_dat.txt
Do you have any thoughts on why this is happening? I would like to adjust my
RightTrimFractionparameter because I suspect there are many loci under selection in my dataset. But at the moment, adjusting that parameter has no effect.