Rmarkdown won't knit: missing aesthetics error

Hi, welcome!
When working with ggplot, you don't have to use the $ syntax, since the ggplot() function has the data parameter where you already specify the data frame you are using, try doing something like this

ggplot(GWASRAW, aes(x = BASE_AGE1_R1, y = BIO_MTB_LIPID_CE_R1, color = BASE_SEX_R1))

If you need more specific help, please provide a proper REPRoducible EXample (reprex) illustrating your issue.