R help - Aug 2011 - 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))
??????? r <- c(m$coef)
??????? c( length(r) , r )
????? }
???? apply( GENO , 2 , f1 )
???? }


Thanks,

?Debs

On Aug 30, 2011, at 6:49 PM, Debs Majumdar wrote:
> 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?
How can we tell? You have not offered the code that you used to run  
it. The code you offered runs without difficulty (once I change the  
T's to TRUE's, that is).

> 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))
>         r <- c(m$coef)
>         c( length(r) , r )
>       }
>      apply( GENO , 2 , f1 )
>      }
>
>
> Thanks,
>
>  Debs
>
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> 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

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_stata at yahoo.com>
To: "r-help at r-project.org" <r-help at 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))
??????? r <- c(m$coef)
??????? c( length(r) , r )
????? }
???? apply( GENO , 2 , f1 )
???? }


Thanks,

?Debs