[R] R package: pbatR

[David Winsemius]

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.
>
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David Winsemius, MD
West Hartford, CT