User: UBodenhofer

gravatar for UBodenhofer
UBodenhofer250
Reputation:
250
Status:
Trusted
Location:
Johannes Kepler University, Linz, Austria
Website:
http://www.bioinf.jku.at/
Twitter:
u_bode
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Google Scholar Page
Last seen:
2 months, 2 weeks ago
Joined:
6 years, 1 month ago
Email:
b*********@bioinf.jku.at

Associate Professor in Bioinformatics at Johannes Kepler University, Linz, Austria. Maintainer of the following packages: 'msa', 'kebabs', 'procoil', 'podkat' (Bioconductor) / 'apcluster', 'rococo' (CRAN)

Posts by UBodenhofer

<prev • 46 results • page 1 of 5 • next >
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Answer: A: Error: could not find function "msaConvert"
... Well, as obvious from your sessionInfo() results, you are using R 3.2.4 which is more than two years old. Since Bioconductor binds releases to the latest R version, you only have Bioconductor 3.3, which includes 'msa' version 1.2.1. The msaConvert() function has been introduced in 'msa' version 1.3. ...
written 11 weeks ago by UBodenhofer250
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Comment: C: Error: could not find function "msaConvert"
... I have seen such error messages in the past, and the reason was always that the users read the manual of a newer version than they actually used. So, if you have the latest version, this is a new issue that I will be glad to go into. Please provide a minimal example that produces that error along wi ...
written 11 weeks ago by UBodenhofer250
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Comment: C: Defining populations in a msaClustalOmega alignment
... Sorry, but I don't get the question. I don't know RAxML, but it seems this is not an 'msa' issue, but a matter of how RAxML expects information about populations. Once you have found that out, you can simply change the sequence names in the FASTA file containing the alignment (if that is what RAxML ...
written 3 months ago by UBodenhofer250
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Answer: A: How to get msa output in fasta format
... If you do not want to make the extra way via the msaPrettyPrint() function, you can also directly write to a FASTA file in the following way (which is actually what msaPrettyPrint() does internally; suppose 'aln' is an object containing a multiple alignment): writeXStringSet(as(unmasked(aln), "XSt ...
written 4 months ago by UBodenhofer250
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Answer: A: seqfault wiht msa
... Thanks for reporting this issue! As far as I can see, my suspicion is indeed the vast amount of data. Actually, ClustalW is not made for such excessive amounts of data. I would rather suggest to use ClustalOmega instead. If that does not work via 'msa' either, maybe the last resort is to use stand-a ...
written 4 months ago by UBodenhofer250
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Comment: C: Using msa msaPrettyPrint(): saving multiple alignement fasta file
... Since you cannot run texi2dvi() itself, the problem is not within the 'msa' package. You either have no TeX/LaTeX system installed or it is improperly installed (e.g. the execution paths are not correctly set). I suggest you open a shell/command prompt window, change to the directory  '~/Desktop/' a ...
written 4 months ago by UBodenhofer250
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Comment: C: Using msa msaPrettyPrint(): saving multiple alignement fasta file
... I can only speculate. Maybe try the following: run msaPrettyPrint() with 'output="tex"' and then run texi2pdf() (from the 'tools' package) on that file. That's basically what msaPrettyPrint() does too. If that does not work, then I'll have to look into my package's code. If it does not work either, ...
written 7 months ago by UBodenhofer250
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Answer: A: Status 1 error when using msaPrettyPrint() to make pdfs with MsaAAMultipleAlignm
... Seems like a LaTeX error. I see two possible sources: (1) There is a problem with your TeX system. (2) The LaTeX code created by msaPrettyPrint() cannot be processed successfully. This can happen if the alignment is too large. 101 sequences seems problematic to me, since 101 is more than the number ...
written 8 months ago by UBodenhofer250
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Answer: A: Error in .Primitive("c")(<S4 object of class "IRanges">) : could not find sym
... It seems that it is an installation issue with one of the packages 'msa' depends on. See the following related thread: Question: Error in GRanges: could not find symbol "recursive" in environment of the generic function ...
written 8 months ago by UBodenhofer250
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Answer: A: How do I extract the complete MsaAAMultipleAlignment object to a file
... Reply to question #1: The width is controlled by the global R option 'width' (in line with the print() methods in the 'Biostrings' package). So you can change the number of columns yourself. If you want to avoid this to have a global effect on your R session, you should save the current value and th ...
written 8 months ago by UBodenhofer250

Latest awards to UBodenhofer

Popular Question 4 months ago, created a question with more than 1,000 views. For VariantAnnotation: Performance and memory issues in readVcf
Supporter 15 months ago, voted at least 25 times.
Scholar 15 months ago, created an answer that has been accepted. For A: Outputting a multiple alignment to file error: could not find function write.XSt
Popular Question 15 months ago, created a question with more than 1,000 views. For Problem reading VCF file using readVcf from package VariantAnnotation
Scholar 19 months ago, created an answer that has been accepted. For A: Outputting a multiple alignment to file error: could not find function write.XSt
Autobiographer 2.3 years ago, has more than 80 characters in the information field of the user's profile.

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