tibble_to_gwaa.RdConvert tibble with genotypes along with a vector of phenotypes to GenABEL internal raw gwaa.data format.
tibble_to_gwaa(x, sex, trait, progress = 1)
| x | tibble with genotypes as described in the Details section |
|---|---|
| sex | a vector of sex values: 0 - female, 1 - male |
| trait | a vector of trait values |
| progress | report progress every N individuals |
gwaa.data-class object
Convert a tibble with the following shape: test_data <- tibble( chr = c(1), pos = c(1001,1002,1005,1017), snp = c('snp1', 'snp2', 'snp3', 'snp4'), strand = c('u'), ind1 = c(0,1,1,2), id2 = c(2,NA,1,1), john = c(0,0,1,0), jill = c(1,1,1,2), elon = c(2,0,NA,1) where columns from 5 to the end are genotypes and names of the columns are sample/individual names. the `snp` column contains names of the snp markers, `chr` is an integer denoting chromosome, `pos` is the genome-wide position (or chromosome-based position), `strand` is currently ignored, but required as a separate column. Genotypes have to be coded as counts of the MINOR ALLELE: AA - 0, Aa - 1 and aa - 2, NA values are allowed.
Marcin Kierczak <marcin.kierczak_NO_SPAM_scilifelab.se>