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
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