[R-sig-genetics] Bayesian network

[Jombart, Thibaut]

Dear Kevin, 

I am admittedly not into Bayesian networks, but in any case the 10 SNPs limitation sounds a bit surprising. However, the error you encounter is quite package-specific. I think you may want to ask your question directly to deal's maintainer, in case you would not find an answer here. 

I don't know of any package that would implement Bayesian networks specifically for genetic data.

Best regards,

Thibaut.

________________________________________
From: r-sig-genetics-bounces at r-project.org [r-sig-genetics-bounces at r-project.org] On Behalf Of Lu, Kevin [kevin.lu at wur.nl]
Sent: 08 June 2009 17:38
To: r-sig-genetics at r-project.org
Subject: [R-sig-genetics] Bayesian network

Dear all,

I am now trying to use Bayesian network to analyze my SNP data,
associating 20 SNPs with one phenotype (plasma cholesterol levels). I
want to use deal package to find the markov plane of my phenotype. I
have 3575 records. After trying the deal package, I can not go through
coomand----jointprior (). It is said "Error in array(1, Dim) : 'dim'
specifies too large an array".

I reduced the number of SNP to 10 and I can continue.  When I try
"result<-heuristic(my.data1.nw,my.data1,my.data1.prior,restart=2,degree=
10,trace=TRUE)". It was said that "[Heuristic [Autosearch Error in
phi[[y]] : attempt to select less than one element". So, I can not get
the results.

I hope someone could help me with it. Am I using the right package?

Thanks in advance,

Kevin



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