Here's the plik code I ran:
plink --bfile olr_try1 --pheno p3.txt --pheno-name dnum --covar p3.txt
--covar-name a4 --missing-phenotype -9 --R olr2.R
The below function is contained in the olr2.R script.
The data which I input is contained in the binary file named olr_try1.
The response variable (PHENO) and the covariate (COVAR) is contained in the
file p3.txt.
I added the option --R-debug to get the output below.
Thanks,
Debs
----- Original Message -----
From: Debs Majumdar<debs_st...@yahoo.com>
To: "r-help@r-project.org"<r-help@r-project.org>
Cc:
Sent: Tuesday, August 30, 2011 3:49 PM
Subject: Error in evalauating a function
Hi,
I am very new to R. So, pardon my dumb question. I was trying to write my
own function to run a different model (perform an ordered logistic regression)
using the example in website
http://pngu.mgh.harvard.edu/~purcell/plink/rfunc.shtml
But R returns a error `R Error in eval(expr, envir, enclos) : object 's' not
found' when I run it. What am I doing wrong here? Here's what I got from the
debug file.
# Input data
n<- 10
PHENO<- c( 1, 3, 2, 3, 1, 1, 1, 2, 1, 2 )
c<- c( 1, 1, 0, 0, 0, 0, 0, 1, 0, 0 )
COVAR<- matrix( c , nrow = n , byrow=T)
CLUSTER<- c( 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 )
l<- 22
g<- c( 0, 1, 1, 0, 0, 0, 1, 0, 2, 1, 0, 0, 0, 0, 0, 1, 1, 1, 0, 1, 0, 0, 1, 2,
0, 0, 0, 2, 0, 0, 0, 1, 0, 1, 0, 1, 0, 1, 0, 2, 0, 1, 1, 0, 1, 0, 0, 1, 0, 0, 0,
0, 0, 1, 0, 0, 1, 1, -1, -1, 1, 0, 0, 1, 1, -1, 1, 0, 1, 0, 0, 2, 0, 0, 0, 1, 0,
0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 1, 2, 0, 1, 0, 0, 1, 0, 1, 0, 1, 2, 0, 1, 1, 0,
1, 0, 2, 1, 0, 0, 0, 2, 1, 0, 1, 0, 1, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, -1, -1, 0, 1, 0, 0, 0, 2, 0, 1, 0, 0, 0, 2, 0,
1, 1, 2, 0, 0, 1, 0, 1, -1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0,
1, 0, 0, 1, 0, 1, 0, 1, 0, 1, 0, 2, 0, 1, 1, 0, 0, 1, 1, 1, 0, 0, 0, 0, 1, 1, 2,
0, 0, 0, 1, 1, 1, 0, 0 )
GENO<- matrix( g , nrow = n ,byrow=T)
GENO[GENO == -1 ]<- NA
# Function
library(ordinal)
Rplink<- function(PHENO,GENO,CLUSTER,COVAR)
{
f1<- function(s)
{
m<- summary(clm(PHENO ~ s))
