(R coding) Biology dataset, changing specific nucleotide letters to 0 or 1 depending on how close they are to the letter A in a specific row?

Question

really new to coding and trying to figure out how to look at each row, and depending on the values on that row, the one closer in the alphabet gets a 0 while the other one gets a 1.

"Now you will convert the genotype information into a numeric representation that you can analyze mathematically. For each row, you will set the allele closest alphabetically to “A” to be 0 and the other allele to be 1. Thus you will create a matrix of zeros and ones."

I've been going through some R books trying to find a way to do it as well as google searching and cannot find anything.

If anyone has any insight it is much appreciated!

Please give us something to work with: http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example — MichaelChirico, Feb 23 '16 at 03:15
C C C C C G G G C C C C C C A A A A C C C C A A A A A C C G G T T T T T T T G G G G G — subtlehelp001, Feb 23 '16 at 03:26
Give a reproducible example. Even a bioinformatics person has no idea what you are asking, what is in each row? Are you simply trying to go from 'AA' , 'AG' type calls to '00', '01' type calls? — JeremyS, Feb 23 '16 at 03:45
I tried, but the format came out incorrectly. So each row has either 1 or 2 letters, and it spans a length of 100. So if I have a row filled with 50 A's and 50 G's, I want the A's to become 0 and the G's to become 1. — subtlehelp001, Feb 23 '16 at 04:04

score 0 · Answer 1 · answered Feb 23 '16 at 03:25

0

This looks like a homework/assignment question so I'm not going to properly answer it, but hopefully you can get where you're trying to go with the help of

which.min(match(c("Q","G","X"), LETTERS))
[1] 2

and some ifelse syntax.

answered Feb 23 '16 at 03:25

Jonathan Carroll

3,897
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score 0 · Answer 2 · answered Feb 23 '16 at 03:26

Without anything else to go on, here's a stab in the dark at what you're after:

set.seed(130490)
genes <- data.frame(allele1 = sample(LETTERS), allele2 = sample(LETTERS),
                    stringsAsFactors = FALSE)

genes$allele1_num <- with(genes, allele1 > allele2)
genes$allele2_num <- !genes$allele1_num

(R coding) Biology dataset, changing specific nucleotide letters to 0 or 1 depending on how close they are to the letter A in a specific row?

2 Answers2