User: UBodenhofer

gravatar for UBodenhofer
UBodenhofer250
Reputation:
250
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Location:
Johannes Kepler University, Linz, Austria
Website:
http://www.bioinf.jku.at/
Twitter:
u_bode
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Last seen:
5 months, 3 weeks ago
Joined:
7 years 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 • 51 results • page 2 of 6 • next >
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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 15 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 18 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 19 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 19 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 19 months ago by UBodenhofer250
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Comment: C: How do I extract the complete MsaAAMultipleAlignment object to a file
... Excellent, I'm glad you solved it. You can also set 'halfNrow' to -1 or NA, then it prints everything. ...
written 19 months ago by UBodenhofer250
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Comment: C: How do I extract the complete MsaAAMultipleAlignment object to a file
... Are you sure you have used the option 'show="complete"'? When I run my example code from above, I see everything. ...
written 19 months ago by UBodenhofer250
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Comment: C: How do I extract the complete MsaAAMultipleAlignment object to a file
... Well, what you can alsways do is to dump this output to a file using sink(). Here is a code snippet: library(msa) filepath <- system.file("examples", "exampleAA.fasta", package="msa") mySeqs <- readAAStringSet(filepath) myAlignment <- msaClustalW(mySeqs) sink("myAlignment.txt") print(m ...
written 19 months ago by UBodenhofer250
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Answer: A: How do I extract the complete MsaAAMultipleAlignment object to a file
... I am sorry, we currently do not have any functionality for saving clustal files in our 'msa' package. I quickly had a look whether there are other options. I came across the thread "R write alignment MSA" on Biostars. The second option sounds fantastic, but I checked it and it does not seem possible ...
written 19 months ago by UBodenhofer250
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Answer: A: running msa (msa) aborts R session
... In this case, André, I agree that it is a memory issue. If you insist on ClustalW, you may have to resort to the command line version (though I am not convinced that this will work). Maybe you better give ClustalOmega a try, since it is explicitly designed for handling larger data. Sorry that I cann ...
written 20 months ago by UBodenhofer250

Latest awards to UBodenhofer

Popular Question 15 months ago, created a question with more than 1,000 views. For VariantAnnotation: Performance and memory issues in readVcf
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Problem reading VCF file using readVcf from package VariantAnnotation
Scholar 2.2 years ago, created an answer that has been accepted. For A: Outputting a multiple alignment to file error: could not find function write.XSt
Supporter 2.2 years ago, voted at least 25 times.
Scholar 2.5 years ago, created an answer that has been accepted. For A: Outputting a multiple alignment to file error: could not find function write.XSt
Autobiographer 3.2 years ago, has more than 80 characters in the information field of the user's profile.

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