I'm using SNPassoc R package for finding association between data SNPs and a continuous variable outcome. I run the analysis and I got the results; however, I got warning message which is:
Warning in terms.formula(formula, data = data) :
'varlist' has changed (from nvar=3) to new 4 after EncodeVars() -- should no longer happen!
my model is:
model <- WGassociation (continuous variable ~ covariate +covariate+ covariate ,data= data)
model
I don't know what it means and should I worry about it or ignore it? Can you please help me?
This warning message is coming glm, which is used by SNPassoc::WGassociation, see this line on GitHub.
Warning message is saying that it is dropping some variable as it is a linear combination of other existing variables in the model.
To reproduce this warning try below example:
# data
x <- mtcars[, 1:4]
# run model, all good
glm(mpg ~ ., data = x)
# Call: glm(formula = mpg ~ ., data = x)
#
# Coefficients:
# (Intercept) cyl disp hp
# 34.18492 -1.22742 -0.01884 -0.01468
#
# Degrees of Freedom: 31 Total (i.e. Null); 28 Residual
# Null Deviance: 1126
# Residual Deviance: 261.4 AIC: 168
Now add useless combo variable which is constructed from existing variables.
# make a combo var
cyldisp <- x$cyl + x$disp
# run model with combo var, now we get the warning
glm(mpg ~ . + cylmpg, data = x)
# Call: glm(formula = mpg ~ . + cyldisp, data = x)
#
# Coefficients:
# (Intercept) cyl disp hp cyldisp
# 34.18492 -1.22742 -0.01884 -0.01468 NA
#
# Degrees of Freedom: 31 Total (i.e. Null); 28 Residual
# Null Deviance: 1126
# Residual Deviance: 261.4 AIC: 168
# Warning message:
# In terms.formula(formula, data = data) :
# 'varlist' has changed (from nvar=4) to new 5 after EncodeVars() -- should no longer happen!