User: seth redmond

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seth redmond70
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Posts by seth redmond

<prev • 7 results • page 1 of 1 • next >
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unpackVcf not found
... I have some old code that's stopped working since I upgraded to R2.15 due to the unpackVcf method not being found. Is this still in the devel branch? or has it been deprecated completely? Or does anyone know another workaround I can use? thanks -s > vcfScan <- scanVcf(file_name) There ...
written 4.8 years ago by seth redmond70 • updated 4.8 years ago by Valerie Obenchain ♦♦ 6.4k
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Comment: C: scanVcf: FORMAT 'GT' not found
... Urgh, yeah I'd checked the tabs between the columns a hundred times, but I hadn't checked for trailing tabs in the header. thanks for the nudge? -s On 3 Dec 2012, at 18:20, Valerie Obenchain wrote: > Hi Seth, > > What version of VariantAnnotation are you using? Please provide the outp ...
written 5.0 years ago by seth redmond70
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scanVcf: FORMAT 'GT' not found
... I keep running into an error in my VCF files but can't seem to pinpoint where the problem is. The file has a number of missing genotypes but nothing that should be causing any problems, I don't think, and it passes vcf-validator without any problem. Completely unremarkable code and head of the file ...
written 5.0 years ago by seth redmond70 • updated 5.0 years ago by Valerie Obenchain ♦♦ 6.4k
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Comment: C: bioconductor on EMR / mapreduce
... Yeah. It was re-installing R and bioC from scratch I was hoping to avoid, really; compiling R / BioC libraries and then storing them in S3 and either copying across or - if possible - running directly from S3. This seems to be what's suggested at the end of that blogpost but not implemented. Possibl ...
written 5.2 years ago by seth redmond70
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Comment: C: bioconductor on EMR / mapreduce
... I'm not too worried about set-up times; once I'd bootstrapped libraries into place I could control the proportion of setup time per node by increasing the granularity - besides, with the volume of data I'm looking at I don't expect it to be a major issue, but having to switch between MPI and hadoop ...
written 5.2 years ago by seth redmond70
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bioconductor on EMR / mapreduce
... I'm trying to install some bioC modules on EC2 / Elastic Mapreduce but I'm running into some library errors when installing (error below). Whilst I could install them locally on each machine, if possible I'd rather avoid the overhead both in terms of bootstrapping the machines, and having to check f ...
dnacopy written 5.2 years ago by seth redmond70 • updated 5.2 years ago by Dan Tenenbaum ♦♦ 8.2k
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KEGGsoap: Space required after the Public Identifier
... I keep running into the same error when trying to do a genes-to- pathways request in the KEGGsoap package: I'm new to the package, but as I understand it I should be able to pass a vector of gene IDs and receive back a vector of pathway IDs, however I keep getting a 'xmlns: URI SOAP/KEGG is not abs ...
keggsoap written 5.9 years ago by seth redmond70 • updated 5.9 years ago by Martin Morgan ♦♦ 20k

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