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I am still new to using R (only a few months), and I am trying to build a Bayesian network (BN) for my research (biology). I have already done all this with discrete variables, however, I am now trying to integrate continuous as well, which I know can be an issue. Right now I'm just building a BN to use in the MoTBFs package to build a hybrid network, using the bnlearn package. Here is my data:

head(training)
Sample rs12913832 rs16891982 rs12203592 rs1800407 rs3829241 rs1805007 rs1408799  rs683 rs3737576
1   1078         CT         GG         GG        CT        GG        CC        GG     TT        TT
2   1254         TT         CC         GG        CC        GG        CC        AG     GG        TT
3   1285         CT         GG         GG        CC        GG        CC        GG     TT        TT
4   1308         CT         GG         GG        CC        AG        CT        AG     GT        TT
5   1382         CC         GG         GG        CC        AA        CT        AG     GT        TT

I have gotten this string below to work as I'm only targeting a few SNPs from the above data:

bn.bayes.Leye<-mmhc(trainingmotbf2[,c(2:6,8,18,26)])

However, it is not creating the correct arcs, so I'm trying to create a whitelist, which looks like this (L is a column not shown in the subset above):

  from         to
1    L rs12913832
2    L  rs1800407
3    L rs16891982
4    L  rs1408799
5    L  rs3829241
6    L rs12203952
7    L rs12896399

When I try to add this whitelist, called white to the bn function:

bn.bayes.Leye<-mmhc(trainingmotbf2[,c(2:6,8,18,26)],whitelist=white)
Error in build.whitelist(whitelist, nodes = names(x), data = x, algo =     method,  : 
  unknown node label present in the whitelist.

Now the error is not cryptic, but all the names in the whitelist are in the data frame. THey show up in the bn that successfully gets created in the whitelist. I've tried the data as factors and characters thinking that had to be a certain format, but same error. What am I missing?

Does anyone have experience or suggested packages for building BN's with a continuous parent and discrete child nodes? Maybe the MoTBFs package is not what I should be using.

GMD886
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1 Answers1

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For anyone interested, I was able to get it work by re-coding how I created the whitelist. Maybe because I used L separately in each case instead of just singlely might have been the issue.

arcs<-data.frame(from="L",to=c("rs12913832","rs16891982","rs12203592","rs1800407","rs12896399","rs3829241","rs1408799"))
GMD886
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