This function accepts the character sex codes accepted by Eigenstrat and turns them into the integer codes accepted by Plink.
Matching is case insensitive.
Cases outside the table below are mapped to 0 (unknown) with a warning.
The correspondence is:
U: 0 (unknown)
M: 1 (male)
F: 2 (female)
sex_to_int(sex)The converted numeric vector of sex codes
Character vector of sex codes
sex_to_char()
Eigenstrat IND format reference: https://github.com/DReichLab/EIG/tree/master/CONVERTF
Plink FAM format reference: https://www.cog-genomics.org/plink/1.9/formats#fam
# verify the mapping above
sex_char <- c('U', 'm', 'f') # mixed case works!
sex_int <- 0:2 # expected values
stopifnot(
all(
sex_to_int( sex_char ) == sex_int
)
)
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