Question: translate DNA sequence to Amino acid sequence in a dataframe
gravatar for XIA.PAN
12 months ago by
XIA.PAN10 wrote:

Dear all,

I have a set of short DNA sequences extracted from a Fastq into a data.frame that need to be translated to amino acids.

After the extraction, they are string characters, need to transfer to DNA string, then translate. So I wrote sth like 

for (n in 1:length(seqs.frame$DNA_seqs))

The translation seems to be working, but how do I put the tranlated amino acids back to the data.frame.

Thank you very much!


ADD COMMENTlink modified 12 months ago by Martin Morgan ♦♦ 21k • written 12 months ago by XIA.PAN10
gravatar for Martin Morgan
12 months ago by
Martin Morgan ♦♦ 21k
United States
Martin Morgan ♦♦ 21k wrote:

No need to iterate, just translate(DNAStringSet(seq.frame$DNA_seqs)). If you first df=DataFrame(seq.frame) then the result of translate() can be placed in the data frame

df$aa = translate(DNAStringSet(df$DNA_seqs))

otherwise use as.character() (again, no iteration) to coerce back to a plain-old-character vector.

ADD COMMENTlink written 12 months ago by Martin Morgan ♦♦ 21k

it worked, thank you Martin.

ADD REPLYlink written 12 months ago by XIA.PAN10
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 143 users visited in the last hour