I'm reading through the vignette on the gwasurvivr R package http://bioconductor.org/packages/devel/bioc/vignettes/gwasurvivr/inst/doc/gwasurvivr_Introduction.html
but I'm finding it not so useful without the specified input files, i.e.
michiganCoxSurv(vcf.file=vcf.file, covariate.file=pheno.file, id.column="ID_2", sample.ids=sample.ids, time.to.event="time", event="event", covariates=c("age", "SexFemale", "DrugTxYes"), inter.term=NULL, print.covs="only", out.file="michigan_only", r2.filter=0.3, maf.filter=0.005, chunk.size=100, verbose=TRUE, clusterObj=NULL)
I would really appreciate if someone could tell me where I could find sample input files for these.
This command is just an example, there are lots of input files there, and I can only make guesses when they show the table through
head and so on.