I want to use GenABEL for GWAS in a diploid plant species, but GenABEL stuck on as it requires a "sex" column in pheno file. It should be filled with "1" for male or "0" for female. But I am working with a plant species. What should I do?
Error in R:
impute <- load.gwaa.data(phe="traits.dat", gen="gen0tped.raw", force=TRUE)
Error in if (length(a) == 1 && !(names(a)[1] == 0 || names(a)[1] == 1)) stop("the column named \"sex\" contains 1 code which is neither 0 (=female) or 1 (=male)") : missing value where TRUE/FALSE needed
From the details section of ?load.gwaa.data:
The first column of the phenotype file MUST contain the subjects' unique ID, named "id"; there should also be a column named "sex" and giving sex information (0 = female, 1 = male). Other columns in the file should contain phenotypic information. Missing values should be coded with "NA"
So try including a sex column with every value as NA.
Also, contact the maintainer (packageDescription("GenABEL", fields = c("Maintainer", "BugReports"))) to explain that GWASs can be done on things where gender isn't relevant.