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Methodology Questions >> How to >> Test for acceleration in one branch, with 2 data p http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1165533861 Message started by eliot on Dec 7th, 2006 at 3:24pm |
Title: Test for acceleration in one branch, with 2 data p Post by eliot on Dec 7th, 2006 at 3:24pm
hi,
You guys have built some very nice tools, thanks. I have a particular problem I'm writing a batch file for, and I'd like to check if I'm doing what I intend to be doing. I have two corresponding datasets from noncoding sequence. One is putatively neutral, and the other putatively functional. (for example they could be an ancestral repeat, and a putative regulatory element which are nearby each other). I want to test if the substitution rate for a particular branch (branch A) in the functional is higher than expected relative to the neutral. I define "expected" based on information external to this data--say the ratio of subsitution rates genome wide. For a 3 species tree ((A,B)C), I put each type of sequence in its own partition, and set up a joint likelyhood function. LikelihoodFunction theLnLik = (neutFilt, neutTree, consFilt, consTree); Then to do a likelyhood ratio test, I get the likelyhood under a constrained model. (I'm using HKY85 by the way). global ss=0; consTree.A.trst:=ss*0.26*neutTree.A.trst; consTree.A.trvs:=ss*0.24*neutTree.A.trvs; consTree.B.trst:=ss*0.68*neutTree.B.trst; consTree.B.trvs:=ss*0.69*neutTree.B.trvs; consTree.C.trst:=ss*0.36*neutTree.C.trst; consTree.C.trvs:=ss*0.35*neutTree.C.trvs; In the second statement, the number 0.26 is a branch specific scaling factor (obtained externally to this data) giving the average ratio between neutral and conserved for branch A transitions. ss is a scaling factor for the level of constraint of this particular element in all branches of the tree. I then compare the likelihood for this model with that for a model with one additional parameter. This parameter allows branch A to go more quickly. global ss=0; global RR=1; RR>1; consTree.A.trst:=ss*RR*0.26*neutTree.A.trst; consTree.A.trvs:=ss*RR*0.24*neutTree.A.trvs; consTree.B.trst:=ss*0.68*neutTree.B.trst; consTree.B.trvs:=ss*0.69*neutTree.B.trvs; consTree.C.trst:=ss*0.36*neutTree.C.trst; consTree.C.trvs:=ss*0.35*neutTree.C.trvs; Is there some problem with my setting RR>1 like this? Are there other problems with how I have written it? What I want to be testing is whether there has been a relaxation of contraint in branch A. thanks much, Eliot |
Title: Re: Test for acceleration in one branch, with 2 da Post by Sergei on Dec 7th, 2006 at 4:37pm
Dear Eliot,
Everything looks OK except that the one sided constraint on 'R' should read: Code (] global R:>1; [/code):
Cheers, Sergei |
Title: Re: Test for acceleration in one branch, with 2 da Post by eliot on Dec 8th, 2006 at 1:46pm
thanks a lot for the help!
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