How to extract two specific patterns before another specific pattern using R?

Question

I am trying to extract both a letter (should be K or Y) and all digits between that letter and the pattern (XO44_TMT6) and put extracted values in two separate columns (Mod.residue and Mod.position.in.pep), but failed to get what I want.

Below are my codes and data frame. Can anyone explain why my codes failed and how to fix that?

Thanks so much!

My data frame:

structure(list(Modifications = c("Y9(XO44_TMT6)", "Y9(XO44_TMT6)", 
"Y9(XO44_TMT6)", "Y9(XO44_TMT6)", "Y9(XO44_TMT6)", "Y9(XO44_TMT6)", 
"Y9(XO44_TMT6)", "Y8(XO44_TMT6)", "Y8(XO44_TMT6)", "Y8(XO44_TMT6)", 
"Y8(XO44_TMT6)", "Y8(XO44_TMT6)", "Y8(XO44_TMT6)", "Y8(XO44_TMT6)", 
"Y8(XO44_TMT6)", "Y8(XO44_TMT6)", "Y8(XO44_TMT6)", "Y8(XO44_TMT6)", 
"Y8(XO44_TMT6)", "Y8(XO44_TMT6)", "Y8(XO44_TMT6)", "Y8(XO44_TMT6)", 
"Y8(XO44_TMT6)", "Y7(XO44_TMT6); M9(Oxidation)", "Y7(XO44_TMT6); M8(Oxidation)", 
"Y7(XO44_TMT6); M8(Oxidation)", "Y7(XO44_TMT6); C9(Carbamidomethyl); C18(Carbamidomethyl)", 
"Y7(XO44_TMT6); C15(Carbamidomethyl)", "Y7(XO44_TMT6)", "Y7(XO44_TMT6)", 
"Y7(XO44_TMT6)", "Y7(XO44_TMT6)", "Y7(XO44_TMT6)", "Y7(XO44_TMT6)", 
"Y7(XO44_TMT6)", "Y7(XO44_TMT6)", "Y7(XO44_TMT6)", "Y7(XO44_TMT6)", 
"Y7(XO44_TMT6)", "Y7(XO44_TMT6)", "Y7(XO44_TMT6)", "Y7(XO44_TMT6)", 
"Y7(XO44_TMT6)", "Y7(XO44_TMT6)", "Y7(XO44_TMT6)", "Y7(XO44_TMT6)", 
"Y7(XO44_TMT6)", "Y7(XO44_TMT6)", "Y7(XO44_TMT6)", "Y7(XO44_TMT6)", 
"Y7(XO44_TMT6)", "Y7(XO44_TMT6)", "Y7(XO44_TMT6)", "Y7(XO44_TMT6)", 
"Y6(XO44_TMT6); C23(Carbamidomethyl)", "Y6(XO44_TMT6); C12(Carbamidomethyl)", 
"Y6(XO44_TMT6); C12(Carbamidomethyl)", "Y6(XO44_TMT6)", "Y6(XO44_TMT6)", 
"Y6(XO44_TMT6)", "Y6(XO44_TMT6)", "Y6(XO44_TMT6)", "Y6(XO44_TMT6)", 
"Y6(XO44_TMT6)", "Y6(XO44_TMT6)", "Y6(XO44_TMT6)", "Y6(XO44_TMT6)", 
"Y6(XO44_TMT6)", "Y6(XO44_TMT6)", "Y5(XO44_TMT6)", "Y5(XO44_TMT6)", 
"Y5(XO44_TMT6)", "Y5(XO44_TMT6)", "Y5(XO44_TMT6)", "Y5(XO44_TMT6)", 
"Y5(XO44_TMT6)", "Y5(XO44_TMT6)", "Y5(XO44_TMT6)", "Y5(XO44_TMT6)", 
"Y5(XO44_TMT6)", "Y5(XO44_TMT6)", "Y5(XO44_TMT6)", "Y5(XO44_TMT6)", 
"Y5(XO44_TMT6)", "Y5(XO44_TMT6)", "Y5(XO44_TMT6)", "Y4(XO44_TMT6); C29(Carbamidomethyl)", 
"Y4(XO44_TMT6); C13(Carbamidomethyl)", "Y4(XO44_TMT6)", "Y4(XO44_TMT6)", 
"Y4(XO44_TMT6)", "Y4(XO44_TMT6)", "Y4(XO44_TMT6)", "Y4(XO44_TMT6)", 
"Y4(XO44_TMT6)", "Y4(XO44_TMT6)", "Y4(XO44_TMT6)", "Y4(XO44_TMT6)", 
"Y4(XO44_TMT6)", "Y3(XO44_TMT6); M5(Oxidation)", "Y3(XO44_TMT6); C11(Carbamidomethyl)", 
"Y3(XO44_TMT6)", "Y3(XO44_TMT6)", "Y3(XO44_TMT6)", "Y3(XO44_TMT6)", 
"Y3(XO44_TMT6)", "Y3(XO44_TMT6)", "Y3(XO44_TMT6)", "Y3(XO44_TMT6)", 
"Y3(XO44_TMT6)", "Y3(XO44_TMT6)", "Y3(XO44_TMT6)", "Y3(XO44_TMT6)", 
"Y3(XO44_TMT6)", "Y3(XO44_TMT6)", "Y3(XO44_TMT6)", "Y3(XO44_TMT6)", 
"Y3(XO44_TMT6)", "Y3(XO44_TMT6)", "Y3(XO44_TMT6)", "Y3(XO44_TMT6)", 
"Y3(XO44_TMT6)", "Y3(XO44_TMT6)", "Y3(XO44_TMT6)", "Y3(XO44_TMT6)", 
"Y3(XO44_TMT6)", "Y3(XO44_TMT6)", "Y3(XO44_TMT6)", "Y3(XO44_TMT6)", 
"Y29(XO44_TMT6)", "Y25(XO44_TMT6)", "Y25(XO44_TMT6)", "Y25(XO44_TMT6)", 
"Y23(XO44_TMT6)", "Y22(XO44_TMT6)", "Y22(XO44_TMT6)", "Y22(XO44_TMT6)", 
"Y22(XO44_TMT6)", "Y22(XO44_TMT6)", "Y22(XO44_TMT6)", "Y22(XO44_TMT6)", 
"Y21(XO44_TMT6)", "Y20(XO44_TMT6)", "Y20(XO44_TMT6)", "Y20(XO44_TMT6)", 
"Y20(XO44_TMT6)", "Y20(XO44_TMT6)", "Y20(XO44_TMT6)", "Y20(XO44_TMT6)", 
"Y20(XO44_TMT6)", "Y2(XO44_TMT6); C8(Carbamidomethyl)", "Y2(XO44_TMT6); C19(Carbamidomethyl)", 
"Y2(XO44_TMT6); C15(Carbamidomethyl)", "Y2(XO44_TMT6); C15(Carbamidomethyl)", 
"Y2(XO44_TMT6); C15(Carbamidomethyl)", "Y2(XO44_TMT6); C15(Carbamidomethyl)", 
"Y2(XO44_TMT6); C15(Carbamidomethyl)", "Y2(XO44_TMT6)", "Y2(XO44_TMT6)", 
"Y2(XO44_TMT6)", "Y2(XO44_TMT6)", "Y2(XO44_TMT6)", "Y2(XO44_TMT6)", 
"Y2(XO44_TMT6)", "Y2(XO44_TMT6)", "Y2(XO44_TMT6)", "Y2(XO44_TMT6)", 
"Y2(XO44_TMT6)", "Y2(XO44_TMT6)", "Y2(XO44_TMT6)", "Y2(XO44_TMT6)", 
"Y2(XO44_TMT6)", "Y2(XO44_TMT6)", "Y19(XO44_TMT6)", "Y19(XO44_TMT6)", 
"Y19(XO44_TMT6)", "Y19(XO44_TMT6)", "Y19(XO44_TMT6)", "Y18(XO44_TMT6)", 
"Y18(XO44_TMT6)", "Y18(XO44_TMT6)", "Y18(XO44_TMT6)", "Y18(XO44_TMT6)", 
"Y18(XO44_TMT6)", "Y18(XO44_TMT6)", "Y17(XO44_TMT6)", "Y17(XO44_TMT6)", 
"Y17(XO44_TMT6)", "Y17(XO44_TMT6)", "Y17(XO44_TMT6)", "Y16(XO44_TMT6)", 
"Y16(XO44_TMT6)", "Y16(XO44_TMT6)", "Y16(XO44_TMT6)", "Y16(XO44_TMT6)", 
"Y16(XO44_TMT6)", "Y16(XO44_TMT6)", "Y16(XO44_TMT6)", "Y16(XO44_TMT6)", 
"Y16(XO44_TMT6)", "Y15(XO44_TMT6); C16(Carbamidomethyl)", "Y15(XO44_TMT6)", 
"Y15(XO44_TMT6)", "Y15(XO44_TMT6)", "Y15(XO44_TMT6)", "Y15(XO44_TMT6)", 
"Y15(XO44_TMT6)", "Y15(XO44_TMT6)", "Y15(XO44_TMT6)", "Y15(XO44_TMT6)", 
"Y14(XO44_TMT6); C15(Carbamidomethyl)", "Y14(XO44_TMT6); C15(Carbamidomethyl)", 
"Y14(XO44_TMT6)", "Y14(XO44_TMT6)", "Y14(XO44_TMT6)", "Y13(XO44_TMT6)", 
"Y13(XO44_TMT6)", "Y13(XO44_TMT6)", "Y12(XO44_TMT6); C14(Carbamidomethyl)", 
"Y12(XO44_TMT6)", "Y12(XO44_TMT6)", "Y12(XO44_TMT6)", "Y12(XO44_TMT6)", 
"Y12(XO44_TMT6)", "Y12(XO44_TMT6)", "Y12(XO44_TMT6)", "Y12(XO44_TMT6)", 
"Y12(XO44_TMT6)", "Y12(XO44_TMT6)", "Y12(XO44_TMT6)", "Y12(XO44_TMT6)", 
"Y11(XO44_TMT6)", "Y11(XO44_TMT6)", "Y11(XO44_TMT6)", "Y11(XO44_TMT6)", 
"Y11(XO44_TMT6)", "Y11(XO44_TMT6)", "Y11(XO44_TMT6)", "Y10(XO44_TMT6)", 
"Y10(XO44_TMT6)", "Y10(XO44_TMT6)", "Y10(XO44_TMT6)", "Y10(XO44_TMT6)", 
"Y10(XO44_TMT6)", "Y10(XO44_TMT6)", "Y10(XO44_TMT6)", "Y10(XO44_TMT6)", 
"Y10(XO44_TMT6)", "Y10(XO44_TMT6)", "Y10(XO44_TMT6)", "Y1(XO44_TMT6); C9(Carbamidomethyl)", 
"Y1(XO44_TMT6); C15(Carbamidomethyl)", "Y1(XO44_TMT6); C15(Carbamidomethyl)", 
"Y1(XO44_TMT6); C15(Carbamidomethyl)", "Y1(XO44_TMT6); C15(Carbamidomethyl)", 
"Y1(XO44_TMT6); C11(Carbamidomethyl)", "Y1(XO44_TMT6); C11(Carbamidomethyl)", 
"Y1(XO44_TMT6); C11(Carbamidomethyl)", "Y1(XO44_TMT6)", "Y1(XO44_TMT6)", 
"Y1(XO44_TMT6)", "Y1(XO44_TMT6)", "Y1(XO44_TMT6)", "Y1(XO44_TMT6)", 
"Y1(XO44_TMT6)", "Y1(XO44_TMT6)", "Y1(XO44_TMT6)", "Y1(XO44_TMT6)", 
"Y1(XO44_TMT6)", "Y1(XO44_TMT6)", "Y1(XO44_TMT6)", "Y1(XO44_TMT6)", 
"Y1(XO44_TMT6)", "N-Term(Prot)(Met-loss+Acetyl); Y9(XO44_TMT6)", 
"N-Term(Prot)(Met-loss+Acetyl); Y9(XO44_TMT6)", "N-Term(Prot)(Met-loss+Acetyl); Y9(XO44_TMT6)", 
"N-Term(Prot)(Met-loss+Acetyl); Y9(XO44_TMT6)", "N-Term(Prot)(Met-loss+Acetyl); Y8(XO44_TMT6)", 
"N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6); C17(Carbamidomethyl)", 
"N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6); C17(Carbamidomethyl)", 
"N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6); C17(Carbamidomethyl)", 
"N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6); C17(Carbamidomethyl)", 
"N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6); C17(Carbamidomethyl)", 
"N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6); C17(Carbamidomethyl)", 
"N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6); C17(Carbamidomethyl)", 
"N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6); C17(Carbamidomethyl)", 
"N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6); C17(Carbamidomethyl)", 
"N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6); C17(Carbamidomethyl)", 
"N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6); C17(Carbamidomethyl)", 
"N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6); C17(Carbamidomethyl)", 
"N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6); C17(Carbamidomethyl)", 
"N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6); C17(Carbamidomethyl)", 
"N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6); C17(Carbamidomethyl)", 
"N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6)", "N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6)", 
"N-Term(Prot)(Met-loss+Acetyl); K4(XO44_TMT6)", "N-Term(Prot)(Met-loss); Y8(XO44_TMT6)", 
"N-Term(Prot)(Met-loss); Y8(XO44_TMT6)", "N-Term(Prot)(Met-loss); Y8(XO44_TMT6)", 
"N-Term(Prot)(Met-loss); Y8(XO44_TMT6)"), Mod.residue = c("9", 
"9", "9", "9", "9", "9", "9", "8", "8", "8", "8", "8", "8", "8", 
"8", "8", "8", "8", "8", "8", "8", "8", "8", "7", "7", "7", "7", 
"7", "7", "7", "7", "7", "7", "7", "7", "7", "7", "7", "7", "7", 
"7", "7", "7", "7", "7", "7", "7", "7", "7", "7", "7", "7", "7", 
"7", "6", "6", "6", "6", "6", "6", "6", "6", "6", "6", "6", "6", 
"6", "6", "6", "5", "5", "5", "5", "5", "5", "5", "5", "5", "5", 
"5", "5", "5", "5", "5", "5", "5", "4", "4", "4", "4", "4", "4", 
"4", "4", "4", "4", "4", "4", "4", "3", "3", "3", "3", "3", "3", 
"3", "3", "3", "3", "3", "3", "3", "3", "3", "3", "3", "3", "3", 
"3", "3", "3", "3", "3", "3", "3", "3", "3", "3", "3", "9", "5", 
"5", "5", "3", "2", "2", "2", "2", "2", "2", "2", "1", "0", "0", 
"0", "0", "0", "0", "0", "0", "2", "2", "2", "2", "2", "2", "2", 
"2", "2", "2", "2", "2", "2", "2", "2", "2", "2", "2", "2", "2", 
"2", "2", "2", "9", "9", "9", "9", "9", "8", "8", "8", "8", "8", 
"8", "8", "7", "7", "7", "7", "7", "6", "6", "6", "6", "6", "6", 
"6", "6", "6", "6", "5", "5", "5", "5", "5", "5", "5", "5", "5", 
"5", "4", "4", "4", "4", "4", "3", "3", "3", "2", "2", "2", "2", 
"2", "2", "2", "2", "2", "2", "2", "2", "2", "1", "1", "1", "1", 
"1", "1", "1", "0", "0", "0", "0", "0", "0", "0", "0", "0", "0", 
"0", "0", "1", "1", "1", "1", "1", "1", "1", "1", "1", "1", "1", 
"1", "1", "1", "1", "1", "1", "1", "1", "1", "1", "1", "1", "9", 
"9", "9", "9", "8", "7", "7", "7", "7", "7", "7", "7", "7", "7", 
"7", "7", "7", "7", "7", "7", "7", "7", "4", "8", "8", "8", "8"
), Mod.position.in.pep = c("", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "")), row.names = c(NA, -300L), class = "data.frame")

My codes:

df <- df.test %>% 
  mutate(Mod.residue = gsub(".*(\\w{1})\\d*\\(XO44_TMT6)\\;*\\s*.*", "\\1", Modifications),
         Mod.position.in.pep = gsub(".*\\w{1}(\\d*)\\(XO44_TMT6\\)\\;*\\s*.*", "\\1", Modifications)
           )

I just realised I already answered a (different) question of yours regarding separation/concatenation of text across columns. I strongly recommend you get a good grip of the AWESOME `tidyr` package: https://tidyr.tidyverse.org/ For string manipulation, I also think `stringr` is much more consistent and easier to use than base R functions: https://stringr.tidyverse.org/ — GuedesBF, Sep 07 '21 at 22:17
Thanks so much for the recommendation! Will learn how to use `tidyr` package. — Chemist learns to code, Sep 07 '21 at 22:30
I just posted a follow-up, similar question to see if somone comes up with something better: https://stackoverflow.com/questions/69095697/extract-all-matches-of-a-pattern-and-concatenate-output-with-mutate — GuedesBF, Sep 08 '21 at 00:19

GuedesBF · Accepted Answer · 2021-09-08T00:18:17.600

2

I think your are looking for tidyr::extract, which fits perfectly for your purpose in a single function call.

library(tidyr)

output_extract<-df %>%
        extract(Modifications,
               into = c('Mod.residue', 'Mod.position.in.pep'),
               regex = ".*([A-Z])(\\d+)(?=\\(XO44_TMT6\\)).*",
               remove=FALSE)

If you want to keep using gsub, you can do it like this (same pattern, two different replacements(\\1 and \\2):

output_gsub<-df %>% mutate(Mod.residue=gsub(".*([A-Z])(\\d+)(\\(XO44_TMT6\\)).*", "\\1", Modifications),
              Mod.position.in.pep=gsub(".*([A-Z])(\\d+)(\\(XO44_TMT6\\)).*", "\\2", Modifications))

These methods give the same outputs:

identical(output_extract, output_gsub)

[1] TRUE

You may want to convert the "Mod.position.in.pep" variable to numeric with as.numeric afterwards.

Unique values for the output columns:

$Mod.residue
[1] "Y" "K"

$Mod.position.in.pep
 [1] "9"  "8"  "7"  "6"  "5"  "4"  "3"  "29" "25" "23" "22" "21" "20" "2"  "19" "18" "17" "16" "15" "14" "13" "12" "11" "10" "1"

EDIT

This will only work whe there is a single match for "Mod.residue" or "Mod.position.in.pep".

If you have multiple "[KY]digit(XO44_TMT6)" per observation, you may have to take a more complex approach, with mutate %>% unnest_wider %>% unite

#Example data
df<-tibble(Modifications="K4(XO44_TMT6); Y6(XO44_TMT6)")

#solution
library(dplyr)
library(tidyr)
library(stringr)

df %>% mutate(Mod.residue=str_extract_all(Modifications, "[A-Z]+(?=\\d+\\(XO44_TMT6\\))"),
              Mod.position.in.pep=str_extract_all(Modifications, "\\d+(?=\\(XO44_TMT6\\))"))%>%
        unnest_wider(col='Mod.residue', names_sep = "_")%>%
        unnest_wider(col='Mod.position.in.pep', names_sep = "_")%>%
        unite(starts_with('Mod.residue'), col="Mod.residue", sep = ';', remove=TRUE, na.rm=TRUE)%>%
        unite(starts_with('Mod.position'), col='Mod.position.in.pep', sep=';', remove=TRUE, na.rm=TRUE)

Output

# A tibble: 1 x 3
  Modifications                Mod.residue Mod.position.in.pep
  <chr>                        <chr>       <chr>              
1 K4(XO44_TMT6); Y6(XO44_TMT6) K;Y         4;6

edited Sep 08 '21 at 00:18

answered Sep 07 '21 at 16:43

GuedesBF

8,409
5
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37

1

Thanks for your answer! Your codes work if e.g., `Y2(XO44_TMT6)` is before `C19(Carbamidomethyl);` but won't work in the case of `C19(Carbamidomethyl); Y2(XO44_TMT6)`. Easy to fix though. – Chemist learns to code Sep 07 '21 at 17:06
Do you happen to know how to extract what I want with `gsub`? – Chemist learns to code Sep 07 '21 at 17:09
Got the regex right for gsub. Updated. Working on `extract` – GuedesBF Sep 07 '21 at 17:35
`extract` is now fine too, @Dr. ChemBio – GuedesBF Sep 07 '21 at 17:41
Sorry, one more question! If there is more than 1 match, how to get all with `extract`? Thanks – Chemist learns to code Sep 07 '21 at 18:27
With extract, you must define N groups to match with the regex, and N columns to spread the output. If you have z matches, the argument `into` should be length z. – GuedesBF Sep 07 '21 at 18:34
Please elaborate on the "more than one match issue" – GuedesBF Sep 07 '21 at 18:34
like in the case of `K4(XO44_TMT6); Y6(XO44_TMT6)`, with the above codes only `Y` and `6` go to the 'Mod.residue' and 'Mod.position.in.pep', respectively. Is it possible to extract "K;Y" and "4;6" into the corresponding columns? – Chemist learns to code Sep 07 '21 at 18:42
hum, this is tricky. I would suggest looking into methods to split strings into rows: https://stackoverflow.com/questions/64608726/convert-numbers-in-comma-separated-string-within-a-data-table-column-into-a-long before the `extract` step – GuedesBF Sep 07 '21 at 18:55
https://stackoverflow.com/questions/33446921/split-a-string-in-each-row-and-duplicate-that-row https://stackoverflow.com/questions/25401505/splitting-a-string-into-new-rows-in-r – GuedesBF Sep 07 '21 at 18:58
Found a solution for your multiple matches: – GuedesBF Sep 07 '21 at 23:12
I edited to include an answer to your dual-observations-per-value-example – GuedesBF Sep 07 '21 at 23:48
Awesome! I really appreciate your help! One more question though. Now running the edited codes generate a new issue: e.g., it will generate something like `Y;NA` and '8;NA' when there is a single match. – Chemist learns to code Sep 08 '21 at 00:11
1

You have to add a `na.rm=TRUE` argument to `unite()` updated – GuedesBF Sep 08 '21 at 00:17

score 2 · Answer 2 · answered Sep 07 '21 at 16:53

2

I would first create a column in which the whole residue inscl. the position is extracted. Then you can separate the name and the position based on this column and remove the intermediate result afterwards:

df.test %>% 
  mutate(
    residue = Modifications %>% str_extract("[KY][0-9]+"),
    Mod.residue = residue %>% str_extract("^[KY]"),
    Mod.position.in.pep = residue %>% str_extract("[0-9]") %>% as.numeric(),
  ) %>%
  select(-residue)

str_extract is designed to work with the other tidyverse functions.

answered Sep 07 '21 at 16:53

danlooo

10,067
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Thanks! Do you happen to know how to extract what I want with `gsub`? – Chemist learns to code Sep 07 '21 at 17:09
`gsub` is for substitution and not for extracting strings. – danlooo Sep 07 '21 at 17:13

How to extract two specific patterns before another specific pattern using R?

2 Answers2

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