I wish to run a very simple logistic regression in R on a case/control GWAS set.
I don't want to use an R package just yet as I prefer to know exactly what is going on.
I am thinking that I should do this using the glm() function where:
model <- glm(phenotype~genotype)
My phenotype is simple binary case control data. My problem is I don't understand the use of family and link functions within the glm function.
Should the model be run as above or:
model <- glm(phenotype~genotype, family=binomial())
model <- glm(phenotype~genotype, family=binomial("logit"))
or perhaps none of the above?