[R] glmnet for Binary trait analysis

Noah noah.hu at hotmail.com
Wed Sep 21 02:25:12 CEST 2011


I got an error message saying 

Error in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs,  : 
  NA/NaN/Inf in foreign function call (arg 5)

when I try to analysis a binary trait using glmnet(R) by running the
following code

Xori <- read.table("c:\\SNP.txt", sep='\t');
Yori <- read.table("c:\\Trait.txt", sep=',');
fit1=glmnet(X, Y, family="binomial");

in the above, X is a matrix with values 1, 0, and -1; Y is a one column
matrix with values 1 and 0.

I know how to analysis continuous traits using glmnet, but I have no idea
about how to do it for binary dependent variables. I will appreciate it if
you would give me any suggestion about this error or provide an example code
for handling binary trait using glmnet. 

Looking forward for your kindly help.



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