Error while fetching sequence and preparing proteome about daglogo HOT 5 OPEN

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from daglogo.

Hi @hassanakthv ,

I updated the development version of dagLogo to fix this issue. You can try to install it via
BiocManager::install("jianhong/dagLogo")

Let me know if it does not work for you.

Jianhong.

from daglogo.

Hello,
I am trying to use dagLogo for a Motif analysis, and meet a error when running fetchSequence function.

The sequence length is 12 for all 59 peptides in data file dat3, here is my codes,

seq <- fetchSequence(toupper(as.character(dat3$ProteinID)),
type="uniprotswissprot",
anchorAA="*",
anchorPos=as.character(dat3$M_Sequence),
proteome = proteome,
upstreamOffset=7,
downstreamOffset=7)

Error:
Error in rep(seq.int(nrow(dat)), lengths(anchorPos)) :
invalid 'times' argument

I use the latest version of dagLogo, and also tried your development version BiocManager::install("jianhong/devtools"), but the error still occurs. Could you kindly help have a look? If you need more information please let me know. Thank you very much.

Best wishes,

Zhaowei

from daglogo.

@mengatron ,
Could you please share me the minimized sample code to repeat your error?
Jianhong.

from daglogo.

Hello Jianhong, thank you for your help, here is a minimized sample code,

  | X | ProteinID | Sequence | M_Sequence | Lenght

1 | 4 | A0MZ66 | EQAIGEYEDLR | EQAIGEYEDLR | 12
2 | 20 | O00273 | KTETVQEACER | KTETVQEACER | 12
3 | 31 | O00273 | ASPPGDLQNPK | ASPPGDLQNPK | 12
4 | 32 | O00273 | ALAVALNWDIK | ALAVALNWDIK | 12
5 | 34 | O00273 | LQQTQSLHSLR | LQQTQSLHSLR | 12
6 | 45 | O60271 | GGETPGSEQWK | GGETPGSEQWK | 12
7 | 50 | O60271 | DVAGLDTEGSK | DVAGLD*TEGSK | 12

Note: there is a sign of * to the right side of the sixth amino acid (anchorAA) for each sequence in column "M_Sequence", as shown for the last sequence DVAGLD*TEGSK, but when I send my comment most of * disappeared except for the last one.

By the way, here is my code for creating the proteome,

proteome <- prepareProteome(fasta = system.file("extdata", "HUMAN.fasta", package = "dagLogo"), species = "Homo sapiens")

Please tell me if you need anything more, thanks.

Zhaowei

from daglogo.