[BioC] what is the best way to correlate SFP data to a phylogenetic correlation? (fwd)

[Justin Borevitz]

Hi, great question and a powerful approach.  My first thought is to consider
the traits separately, # of hosts and virulence. Then consider SFP
haplotypes throughout the genome in sliding windows, but blocks would be
preferred. You need to associate a plasmodium haplotypes with the
quantitative trait across strains and then scan the genome.  Your null can
be shuffled phenotypes vs true haplotypes to determine a genome wide FDR. 

I've been measuring pairwise diversity and total SFP counts (and their
difference Tajimas D like) thinking about patterns of selection on the
genome but this measure isn't what you want for an association. It could
however give some clues as to what might be going on. I'm sure you've seen
recent papers by Kim et al Kidgell et al.

Good luck! (the more diverse strains with good tests of host range/virulance
the better >100)

Justin

-----
Justin Borevitz
http://naturalsystems.org/lab 
-----Original Message-----
From: Charles C. Berry [mailto:cberry at tajo.ucsd.edu] 
Sent: Monday, April 09, 2007 10:18 AM
To: Justin Borevitz
Subject: [BioC] what is the best way to correlate SFP data to a phylogenetic
correlation? (fwd)
Justin,
Did you see this? I did not see any traffic on bioc in response.
Best,
Chuck
Charles C. Berry                        (858) 534-2098
                                         Dept of Family/Preventive Medicine
E mailto:cberry at tajo.ucsd.edu	         UC San Diego
http://biostat.ucsd.edu/~cberry/         La Jolla, San Diego 92093-0901
---------- Forwarded message ----------
Date: Thu, 5 Apr 2007 19:20:29 -0700 (PDT)
From: lgilbert at berkeley.edu
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] what is the best way to correlate SFP data to a phylogenetic
     correlation?

I don't know where to start:
I'm planning on generating a single feature polymorphism (SFP) map for 11
primate strains of malaria using a high density array. Some previous work
on these primate malarias found a significant negative correlation between
a quantitative measure of virulence and the number of host species each
primate malaria could infect using a least squares model.
I want to somehow test or establish an association with the SFP divergence
score for genes implicated in host specificity to this other data- the
host number-virulence correlation. I don't know what would be the best
statistical approach- some likelihood method, a multivariate correlation?
Sincerely,
Betty