If you want to use subset
, you could try:
subset(df, !duplicated(subset(df, select=c(allrl, RAW.PVAL))))
# RAW.PVAL GR allrl Bak
#1 0.05 fr EN1 B12
#3 0.45 fr EN2 B10
#4 0.35 fg EN2 B066
But, I think @thelatemail’s approach would be better
df[!duplicated(df[c("RAW.PVAL","allrl")]),]