Dear experts, I am trying to perform an association using snpStats. I have a snp matrix called 'plink' which contains my genotype data (as a list of $genotypes, $map, $fam), and a phenotype data frame which contains the outcomes (outcome1, outcome2,...) I would like to associate with the genotype. My question is, how do I loop through the outcomes? This type of data seems different from all the others and I am having trouble manipulating it, so I would also be grateful if you have suggestions of some tutorials that can help me understand how to do this and other manipulations such as subsetting the snp.matrix data for example.
This is what I have tried for the loop: rhs <- function(x) { x<- snp.rhs.tests(x, family="gaussian", data=phenotype, snp.data=snp.matrix$genotype) } res_ <- apply(phenotype,2,rhs) Error in x$terms : $ operator is invalid for atomic vectors Then I tried this: for (cov in names(phenotype)) { association<-snp.rhs.tests(cov, family="gaussian",data=phenotype, snp.data=snp.matrix$genotype) } Error in eval(expr, envir, enclos) : object 'outcome1' not found Thank you as usual for your help! -f -- View this message in context: http://r.789695.n4.nabble.com/loop-through-columns-in-S4-objects-tp4104836p4104836.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help@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.