Just to be sure, you do know that in R, 6:9 creates a vector c(6,7,8,9)? If you want to select row 22 and column 6 you would write $PE[22,6].
Anyway, it's hard to understand what the problem is without data to reproduce it. Could you provide a reprex. This summary() function always prints a lot, but still returns a PE dataframe that could be subsetted appropriately.