I am guessing (from other evidence of lapses in attention to
documentation) that you failed to pay attention when you encountered
these sentences on the page you offered a link to:
"For analysis, this package provides a frontend to the PBAT software"
"For analysis, users must download PBAT (developed by Christoph Lange)
and accept it's license, available on the PBAT webpage."
--
david.
On Jul 14, 2011, at 11:05 AM, Lisa wrote:
> Dear All,
>
> Does anybody have experience with R package pbatR
> (http://cran.r-project.org/web/packages/pbatR/index.html)? I am
> trying to
> use it to analyze the family-based case-control data, but the package
> totally doesn?t work on my computer. I contacted the authors of the
> package,
> but I haven?t heard anything from them.
>
> Following the package manual, I tried the simple example as below:
>
> library(pbatR)
> library(tcltk)
> pbat.set("C:/pbat")
>
> x <- data.frame(pid = c(1,1,1,2,2,2,2,3,3,3), # three families
> id = c(1,2,3,1,2,3,4,1,2,3),
> idfath = c(0,0,1,0,0,1,1,0,0,1),
> idmoth = c(0,0,2,0,0,2,2,0,0,2),
> sex = c(1,2,1,1,2,2,2,1,2,1),
> AffectionStatus = c(0,0,1,0,0,1,0,0,0,1), # 1 for case, 0 for
> control
> m1.1 = c(1,1,2,2,1,1,2,2,2,1), # two SNPs with two
> columns
> for each SNP
> m1.2 = c(1,2,1,2,1,2,1,1,2,2),
> m2.1 = c(1,1,2,2,2,1,1,1,2,1),
> m2.2 = c(2,1,2,1,2,2,2,1,1,1))
> x1 <- as.ped(x)
>
> y <- data.frame(pid = c(1,1,1,2,2,2,2,3,3,3),
> id = c(1,2,3,1,2,3,4,1,2,3),
> age = c(55,50,22,38,37,15,11,42,41,17),
> weight = c(185,170,130,165,170,90,60,170,160,120))
> y1 <- as.phe(y)
>
>
> 1. I first consider a model with the disease as a phenotype, and two
> SNPs as
> predictors (on covariates) as bellow:
>
> pbat.m(AffectionStatus ~ NONE, y1, x1, fbat="gee",
> distribution='categorical', offset='none')
>
> But some error messages were returned:
> Error in writeCommandStrMatch("distribution", distribution,
> c("default", :
> 'distribution' can only take on the following values:
'default',
> 'jiang',
> 'murphy', 'naive', 'observed'. You passed the
invalid value
> 'categorical'.
>
> Then I removed last two arguments
> pbat.m(AffectionStatus ~ NONE, y1, x1, fbat="gee")
>
> This time, a box appeared on the console:
> R for Windows GUI front-end has encountered a problem and needs to
> close.
>
> 2. I consider a model with the disease as a phenotype, and two
> covariates
> (age, weigth) and two SNPs as predictors as bellow:
>
> pbat.m(AffectionStatus ~ age + weight, y1, x1, fbat="gee")
>
> The function had been running for a very long time and no output was
> returned until I had to stop it.
>
> Any help would be greatly appreciated.
>
> Thanks.
>
> Lisa
>
>
> --
> View this message in context:
http://r.789695.n4.nabble.com/R-package-pbatR-tp3667844p3667844.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
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> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT