Request: IUPAC with treshold

[spilsberg]

Dear seqinr team

I have a request.

I am designing PCRs for different phylogenetic levels based on a few hundred sequences. For that purpose it had been handy to have a consensus sequence with IUPAC codes generated with a threshold I have chosen.

Test data:

seq1
ATGGCTAGACATTTAAAAT
seq2
ATGGCTAGAGATTTAAAAT
seq3
ATGGCTAGAGATTTAAAAT
seq4
ATGGCTAGAGATTTAAAAT

This is the result I wish for:

consensus(test, method = "IUPAC", threshold = 0.8, warn.non.IUPAC = FALSE, type = "DNA")
atggctagaSatttaaaat
consensus(test, method = "IUPAC", threshold = 0.7, warn.non.IUPAC = FALSE, type = "DNA")
atggctagaGatttaaaat

[simonpenel]

Dear user,

if I understand correctly you want to display as consensus the nucleotide whith the higher frequency if its frequency is above the threshold, and display the IUPAC code representing the different nucleotides at the site otherwise, am I wright?

best,

Simon

[spilsberg]

Dear Simon Thank you for a quick answer Yes you are right As I understand consensus(testMSA, method = "threshold", threshold = 0.X) Given 4 sequences and 3 x A and 1 T in one position threshold 0.7 will call A threshold 0.8 will call N What I want is simply til add the threshold option to the method = “IUPAC” threshold 0.7 will call A threshold 0.8 will call W sincerely Bjørn Vennlig hilsen Bjørn Spilsberg m +47 41105344 ***@***.*** | www.vetinst.no ***@***.*** Fra: Simon Penel ***@***.***> Sendt: mandag 4. november 2024 12:57 Til: lbbe-software/seqinr ***@***.***> Kopi: Spilsberg, Bjørn ***@***.***>; Author ***@***.***> Emne: Re: [lbbe-software/seqinr] Request: IUPAC with treshold (Issue #15) Dear user, if I understand correctly you want to display as consensus the nucleotide whith the higher frequency if its frequency is above the threshold, and display the IUPAC code representing the different nucleotides at the site otherwise, am I wright? best, Simon — Reply to this email directly, view it on GitHub<#15 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AEJH3A7XTCV2USNJBLQICHDZ65OI7AVCNFSM6AAAAABQ55ODNGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINJUGUZDCNBZGA>. You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>>

[simonpenel]

Dear Bjorn

I updated a new version of seqinr.

There is a new optional argument in the consensus function, with the threshold method: "threshold.IUPAC"
For example

phylip <- read.alignment(file = system.file("sequences/test.phylip",
    package = "seqinr"), format = "phylip")
res.thr <- consensus(phylip, method = "threshold",threshold.IUPAC =TRUE )

To use the new version of seqinr:

require("devtools")
install_github("lbbe-software/seqinr")

Let me know if this is convenient for you

Best,

Simon