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branch-specific BS-REL? (Read 3130 times)
Vinny Lynch
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branch-specific BS-REL?
Oct 30th, 2012 at 2:08pm
 
Hi All,

Is there a way to restrict a BS-REL analysis to a particular lineage? I'm not really interested in testing all branches since there is only one I am interested in. I tried looking at the .bf file for BS-REL but it was not obvious to me where I might change something.

Thanks
Vinny

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Vinny Lynch
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Re: branch-specific BS-REL?
Reply #1 - Oct 31st, 2012 at 1:06pm
 
It just occurred to me that targeting a specific lineage for the BS-REL test a priori will not produce different results from running the model on the full dataset (other than saving computational cost and time). So might it be statistically OK to disregard the other lineages and assess the evidence for selection from the LRT and p-value of only my a priori selected lineage (rather than the p_Holm)?
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Sergei
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Re: branch-specific BS-REL?
Reply #2 - Nov 5th, 2012 at 3:34pm
 
Hi Vinny,

This is correct. I am also attaching a file that permits you to select lineages for analysis.

Sergei

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Vinny Lynch
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Re: branch-specific BS-REL?
Reply #3 - Nov 7th, 2012 at 8:19am
 
Hi Sergei,

Thanks for the file, that will certainly help and save your datamonkey servers from analyzing my dataset!

I'm curious which case you find more convincing from these two nested BS-REL analysis.

A dataset of 51 mammalian species with 213 codons where BS-REL identifies positive selection in human with mean omega=10, omega1=0.0008 (P1=0.68), omega2=0.0008 (P2=0.56), and omega3=1000 (p3=0.09) at LRT=5.22 and p-value=0.01.

Or dataset of 18 primate species selected from the larger 51 species dataset where BS-REL identifies positive selection in human with mean omega=10, omega1=5E-9 (P1=0.88), omega2=7.5E-8 (P2=0.03), and omega3=1000 (p3=0.085) at LRT=8.7 and p-value=0.0017.

Both are statistically signifiant and have similar results, but should one always prefer a larger dataset (so long as the alignment is clear)?

Thanks,
Vinny

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Sergei
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Re: branch-specific BS-REL?
Reply #4 - Nov 7th, 2012 at 10:38am
 
Hi Vinny,

I would report both (except in your first example the probabilities add up to > 1); the consclusions are the same: a small proportion of sites (about 9%) is under very strong diversifying selection. Why the different LRT?

1). The analysis may not have fully converged for the alternative model with 51 species.
2). The lineages you added for the large data set may have had enough of an effect on the inference for the human lineage.

Not too much of a concern though.

Sergei

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