R: replacing values in string all at once

Question

I have a data frame that looks like this:

    USequence
# 1 GATCAGATC
# 2 ATCAGAC

I'm trying to create a function that would replace all the G's with C's, A's with T's, C's with G's, and T's with A's:

    USequence
# 1 CTAGTCTAG
# 2 TAGTCTG

This is what I have right now, the function accepts k, a data frame with a column named USequence.

conjugator <- function(k) {
  k$USequence <- str_replace_all(k$USequence,"A","T")
  k$USequence <- str_replace_all(k$USequence,"T","A")
  k$USequence <- str_replace_all(k$USequence,"G","C")
  k$USequence <- str_replace_all(k$USequence,"C","G")
}

However the obvious problem would be that this is doesn't replace the characters at once, but rather in steps which would not return the desired result. Any suggestions? Thanks

Sounds like a variant of the infamous interview question: "Swap A and B without creating a temp variable" :-) — Carl Witthoft
– Carl Witthoft, Commented Jul 18, 2015 at 11:33

akrun · Accepted Answer · 2015-07-18 09:18:02Z

6

You could use chartr

df1$USequence <- chartr('GATC', 'CTAG', df1$USequence)
df1$USequence 
#[1] "CTAGTCTAG" "TAGTCTG"

Or

library(gsubfn)
gsubfn('[GATC]', list(G='C', A='T', T='A', C='G'), df1$USequence)
#[1] "CTAGTCTAG" "TAGTCTG"

answered Jul 18, 2015 at 9:18

akrun

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