How to match characters from strings in R?

Question

Before posting my question, I would just like to mention that I have looked through the "Similar questions" tab, and have not quite found what I am looking for. I found something somewhat similar here, but it is in python. There was also a nice idea here that may help as last resort. In any case, I would like to try first if there is a more straightforward way to do it.

To the problem: Say there are 2 different data frames: (1) Ref_seq; and (2) Variants:

>Ref_seq
   Seq_name                                AA_seq
1      Ref1 VSASTQASRQKKMQEISSLVKYFIKCANRRAPRLKCQ
2      Ref2          SNFPHLVLEKILVSLTMKNCKAAMNFFQ
3      Ref3       RRQKRPSSGTIFNDAFWLDLNYLEVAKVAQS
4      Ref4          HCTSVSKEVEGTSYHESLYNALQSLRDR
5      Ref5     DHTGEYGNLVTIQSFKAEFRLAGGVNLPKIIDC
6      Ref6      HKDQMVDIMRASQDNPQDGIMVKLVVNLLQLS
7      Ref7        SNILLKDILSVRKYWCEISQQQWLELFSVY
8      Ref8      LTIFLKTLAVNFRIRVCELGDEILPTLLYIWT
9      Ref9       EDQSSMNLFNDYPDSSVSDANEPGESQSTIG
10    Ref10       SLSEKSKEETGISLQDLLLEIYRSIGEPDSL

>Variants
  peptideID     AA_seq
1      Pep1 QEISALVKYF
2      Pep2 HTGERGNLVT
3      Pep3 NKMTTSVLIK
4      Pep4 SMNLKNDYPD
5      Pep5 NEPGYSQSTI
6      Pep6 NPQDVIMVKL
7      Pep7 MAAKFNKMTL
8      Pep8 RRQKDPSSGT
9      Pep9 QQQWTELFSV

The first data frame contains the amino acid (aa) sequences from a reference organism, whilst the second contains the aa sequences from a test organism. It is known that the sequences from the Variants object contain at least (a) one aa change, (b) 4 matching characters to the reference sequence from Ref_seq, and (c) the matching can be forward or backwards (e.g. aa sequence from line 3 of Variants).

I am trying to find a way to lookup and retrieve to which reference sequence (Seq_name) each peptideID belongs to. The result should look like this:

  peptideID     AA_seq Seq_name
1      Pep1 QEISALVKYF     Ref1
2      Pep2 HTGERGNLVT     Ref5
3      Pep3 NKMTTSVLIK     Ref2
4      Pep4 SMNLKNDYPD     Ref9
5      Pep5 NEPGYSQSTI     Ref9
6      Pep6 NPQDVIMVKL     Ref6
7      Pep7 MAAKFNKMTL     Ref2
8      Pep8 RRQKDPSSGT     Ref3
9      Pep9 QQQWTELFSV     Ref7

I thought that maybe regex coupled with a loop for each peptideID, considering that the strings change according to it. But I cannot wrap my head around it.

Any help will be very welcome!

Data from the example:

Ref_seq <- data.frame(Seq_name=paste0("Ref",1:10), AA_seq=c("VSASTQASRQKKMQEISSLVKYFIKCANRRAPRLKCQ", "SNFPHLVLEKILVSLTMKNCKAAMNFFQ", "RRQKRPSSGTIFNDAFWLDLNYLEVAKVAQS", "HCTSVSKEVEGTSYHESLYNALQSLRDR", "DHTGEYGNLVTIQSFKAEFRLAGGVNLPKIIDC", "HKDQMVDIMRASQDNPQDGIMVKLVVNLLQLS", "SNILLKDILSVRKYWCEISQQQWLELFSVY", "LTIFLKTLAVNFRIRVCELGDEILPTLLYIWT", "EDQSSMNLFNDYPDSSVSDANEPGESQSTIG", "SLSEKSKEETGISLQDLLLEIYRSIGEPDSL"))
Variants <- data.frame(peptideID=paste0("Pep",1:9), AA_seq=c("QEISALVKYF", "HTGERGNLVT", "NKMTTSVLIK", "SMNLKNDYPD", "NEPGYSQSTI", "NPQDVIMVKL", "MAAKFNKMTL", "RRQKDPSSGT", "QQQWTELFSV"))

Andre Wildberg · Answer 1 · 2021-11-23T21:22:25.733

You can try something like this. It takes the AAs from var and compares them with the ones from Ref_seq, including reverse matching. It uses agrep for fuzzy matching.

data.frame( var, Seq_name=unlist( sapply( var$AA_seq, function(x){ 
  a <- !anyNA(agrep(x, Ref_seq$AA_seq)[1]); 
  ifelse( a, Ref_seq[ agrep(x, Ref_seq$AA_seq)[1],], 
    Ref_seq[ agrep(paste0(rev(strsplit(x, "")[[1]]), 
    collapse=""),Ref_seq$AA_seq)[1], ] ) } ) ) )

  peptideID     AA_seq Seq_name
1      Pep1 QEISALVKYF     Ref1
2      Pep2 HTGERGNLVT     Ref5
3      Pep3 NKMTTSVLIK     Ref2
4      Pep4 SMNLKNDYPD     Ref9
5      Pep5 NEPGYSQSTI     Ref9
6      Pep6 NPQDVIMVKL     Ref6
7      Pep7 MAAKFNKMTL     Ref2
8      Pep8 RRQKDPSSGT     Ref3
9      Pep9 QQQWTELFSV     Ref7

Although this works for this example, I would suggest searching for a Bioconductor library that does what you want. There are many tricky situations that those libraries already solve.

Data

Ref_seq <- structure(list(Seq_name = c("Ref1", "Ref2", "Ref3", "Ref4", "Ref5", 
"Ref6", "Ref7", "Ref8", "Ref9", "Ref10"), AA_seq = c("VSASTQASRQKKMQEISSLVKYFIKCANRRAPRLKCQ", 
"SNFPHLVLEKILVSLTMKNCKAAMNFFQ", "RRQKRPSSGTIFNDAFWLDLNYLEVAKVAQS", 
"HCTSVSKEVEGTSYHESLYNALQSLRDR", "DHTGEYGNLVTIQSFKAEFRLAGGVNLPKIIDC", 
"HKDQMVDIMRASQDNPQDGIMVKLVVNLLQLS", "SNILLKDILSVRKYWCEISQQQWLELFSVY", 
"LTIFLKTLAVNFRIRVCELGDEILPTLLYIWT", "EDQSSMNLFNDYPDSSVSDANEPGESQSTIG", 
"SLSEKSKEETGISLQDLLLEIYRSIGEPDSL")), class = "data.frame", row.names = c("1", 
"2", "3", "4", "5", "6", "7", "8", "9", "10"))

var <- structure(list(peptideID = c("Pep1", "Pep2", "Pep3", "Pep4", 
"Pep5", "Pep6", "Pep7", "Pep8", "Pep9"), AA_seq = c("QEISALVKYF", 
"HTGERGNLVT", "NKMTTSVLIK", "SMNLKNDYPD", "NEPGYSQSTI", "NPQDVIMVKL", 
"MAAKFNKMTL", "RRQKDPSSGT", "QQQWTELFSV")), class = "data.frame", row.names = c("1", 
"2", "3", "4", "5", "6", "7", "8", "9"))

How to match characters from strings in R?

1 Answers1