User: Michael Dondrup

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Posts by Michael Dondrup

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Answer: A: Gviz: Error plotting C.elegans ideogram
... Just found the obvious. The error is caused by the fact that the c.elegans genome doesn't have a cytoband track. Not all genomes have this track. Maybe the error message could be made more clear, something like: "There is no cytoband information for chromosome 1 in UCSC genome 'ce4'" Cheers Michae ...
written 5.5 years ago by Michael Dondrup550
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Gviz: Error plotting C.elegans ideogram
... Hi, I am trying to plot an ideogram track for C. elegans using Gviz. However I cannot generate the ideogram track: > itrack <- IdeogramTrack(genome = "ce6", chromosome = "chrI" ) Error in normArgTrack(track, trackids) : Unknown track: cytoBandIdeo I have tried also "ce4, and ce10" and for t ...
ideogram genomes gviz written 5.5 years ago by Michael Dondrup550
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IRanges: how to emulate findOverlaps(multiple=TRUE)?
... Hi, I have some R-scripts that rely on the argument multiple=TRUE in findOverlaps(). However, this option has been removed in the latest release it seems, as it was said to be deprecated before. But now our scripts don't work any more, and removing the parameter simply yields a different output form ...
written 5.6 years ago by Michael Dondrup550 • updated 5.6 years ago by Michael Lawrence9.8k
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Comment: C: rtracklayer export fails
... So here is the example where export fails: $ R --vanilla > library(rtracklayer) Loading required package: RCurl Loading required package: bitops > library(IRanges) Attaching package: 'IRanges' The following object(s) are masked from 'package:base': cbind, eval, Map, mapply, order, pas ...
written 6.8 years ago by Michael Dondrup550
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Comment: C: rtracklayer export fails
... Yes, it's totally strange it seemed to be something in my session. If I start R --vanilla the simple example works, however I am still struggling with exporting real-size data because it yields the same error message. I will post an example later. Thanks for your help On Feb 19, 2011, at 11:02 PM ...
written 6.8 years ago by Michael Dondrup550
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Comment: C: Problem loading saved GenomicRanges object
... Thank you Vincent, updateObject worked. Best Michael On Feb 20, 2011, at 12:14 PM, Vincent Carey wrote: > It isn't a problem with loading it, but with showing it given the relationship between the object and the class definition in your session. After loading, try > > gr = updateObject ...
written 6.8 years ago by Michael Dondrup550
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Problem loading saved GenomicRanges object
... Hi, I have saved a GRanges object and now after updating GenomicRanges I have trouble loading it again: > gr GRanges with 2581 ranges and 4 elementMetadata values Error in validObject(.Object) : invalid class "GRanges" object: slots in class definition but not in object: "seqinfo" > This d ...
genomicranges written 6.8 years ago by Michael Dondrup550 • updated 6.8 years ago by Vincent J. Carey, Jr.6.2k
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rtracklayer export fails
... Hi, I am trying to use export in the rtracklayer package on R 2.12.1 on MacOS but already the example fails, see below: Best Michael > example(export) export> track <- import(system.file("tests", "v1.gff", package = "rtracklayer")) export> ## Not run: export(track, "my.gff", vers ...
rtracklayer written 6.8 years ago by Michael Dondrup550 • updated 6.8 years ago by Vincent J. Carey, Jr.6.2k
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Comment: C: Transfer Fasta to Fastq
... Yes there is one, just figured out the writeFastQ method for ShortRead. So here is a code example, because it wasn't quite clear for me how to feed the the read454 function with data in the correct way, maybe there should be a better example in the documentation (eg. this ): > rpath = RochePath ...
written 7.1 years ago by Michael Dondrup550
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Comment: C: Transfer Fasta to Fastq
... Hi, if you got fasta + qual files, there is an example perl script here: http://biostar.stackexchange.com/questions/2774/how-to-convert-454 -data-to-sam-format/2778#2778 have nothing in R yet, but that shows the principle and could be easily done in R. If you don't have a qual file, you will have to ...
written 7.1 years ago by Michael Dondrup550

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