How to calculate the p-value (?) using LRT from codeml output ?
0
2
Entering edit mode
5 months ago
sunnykevin97 ▴ 450

HI

I constructed LRT

ΔLRT = 2×(lnL1 - lnL0) 
         = (2×(-1114.093613 − (-1116.287406)) = 4.387586.

The degree of freedom is 1 (np1 - np0 = 20 - 19)  = 1 

How do I calculate the p-value ?

Little confused,

Suggestions please.

alignment DNA Gene RNA • 328 views
ADD COMMENT
1
Entering edit mode

Hey check out this tutorial..

https://evosite3d.blogspot.com/2011/09/identifying-positive-selection-in.html
ADD REPLY
0
Entering edit mode

Seems good tutorial, I'm not so clear ... Clear explanation is needed in understanding/calculating the p-value (?) using the LRT and df score.

ADD REPLY
2
Entering edit mode

Calculating p-value using dchisq() in R.

dchisq(4.387586,1) 
p-value 0.02123465
ADD REPLY

Login before adding your answer.

Traffic: 1148 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6