Grantham Matrix

Fetch_Grantham.R

grantham <- readr::read_tsv("https://gist.githubusercontent.com/danielecook/501f03650bca6a3db31ff3af2d413d2a/raw/5583a134b36b60762be6cd54002a0f4044338cd0/grantham.tsv") %>%
  tidyr:: gather(SECOND,SCORE, -FIRST) %>% dplyr::filter(SCORE > 0)  


calculate_grantham <- function(a1, a2) {
  (grantham %>% dplyr::filter(FIRST == a1, SECOND == a2))$SCORE
}

grantham.tsv

what is this?

uhhh... This is a function I'm putting together in R for calculating grantham scores.

From this article

Grantham scores, which categorize codon replacements into classes of increasing chemical dissimilarity, were designated conservative (0-50), moderately conservative (51-100), moderately radical (101-150), or radical (≥151) according to the classification proposed by Li et al. (28).

These numbers are estimated by looking at the frequency of all pair-wise amino acid substitutions between species. If you look at that distribution, some changes are much more frequent indicating that they are 'tolerable' and don't have much of an effect on protein function. However, some are much less frequent - indicating they likely cause severe changes to proteins.

In Biology we use them to estimate how severe a mutation (or variant) might be when we identify one through genotyping.

I like to use github gist to store little snippets like this until I find a more permanent home for them (e.g. a project).