How do you get the data into R? It works when starting from an Excel sheet using read_excel from the readxl library.
This puts the NA column in backticks.

Maybe other importers can be modified as well.
For example, read_csv(readr / tidyverse) accepts definitions for NA, when you say:
dipeptides = read_csv("Book2.csv", na = "")
you basically excludes "NA" as NA and then its kept as well.
When you have NA in your matrix then you have another problem.
dipeptides = read_csv("Book2.csv", na = "")
Parsed with column specification:
cols(
Sample = col_character(),
AB = col_double(),
BC = col_double(),
GH = col_double(),
JI = col_double(),
KL = col_double(),
`NA` = col_double(),
DG = col_double()
)
>