Moderator: Vincent J. Carey, Jr.

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Posts by Vincent J. Carey, Jr.

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Comment: C: "developing" with HDF5Array
... benchOOM now has getLitGeu() which restores a saved HDF5-backed SummarizedExperiment that is stored in the package ...
written 9 months ago by Vincent J. Carey, Jr.6.2k
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Comment: C: "developing" with HDF5Array
... Excellent.  Thanks very much. ...
written 9 months ago by Vincent J. Carey, Jr.6.2k
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Comment: C: "developing" with HDF5Array
... benchOOM has been updated to include rhconvert, which converts the assay portion of a RangedSummarizedExperiment to HDF5Array (delayed) and returns a SummarizedExperiment with this alternate representation of the assay data.  (rhconvert = "RangedSummarizedExperiment to HDF5 conversion") ...
written 9 months ago by Vincent J. Carey, Jr.6.2k
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Answer: A: "developing" with HDF5Array
... Thanks Hervé.  I am not considering the cases of mixed assay representation, or even multiple assays.  At the moment I am trying to get some realistic performance appraisals of the simple hybrid situation: single large assay in HDF5, everything else in the standard RAM-based representation.   I agre ...
written 9 months ago by Vincent J. Carey, Jr.6.2k
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Tutorial: "developing" with HDF5Array
... I'd like to get some statistics on performance and maintenance issues of using the delayed HDF5 back end for SummarizedExperiments.  This is part of a general project started in the benchOOM package.  In that package I tentatively defined a generic "writeHDF5Dataset" and a method for RangedSummarize ...
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Extension to GoogleGenomics: getVariantCalls
... We have introduced a function, getVariantCalls, into GoogleGenomics, that has the same interface as getVariants, but returns a VRanges with genotype content for all samples. The function has only been tested against the 1000 genomes variant datasets, and at present does not acquire call-related i ...
genetics googlegenomics variants written 10 months ago by Vincent J. Carey, Jr.6.2k
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Comment: C: VariantAnnotation error with readVcf after genotypeToSnpMatrix
... I can't reproduce on several platforms.  Some of your packages seem out of date.  Use library(BiocInstaller); biocValid() and update to a consistent state.  I don't see VariantAnnotation version in your sessionInfo() above. ...
written 12 months ago by Vincent J. Carey, Jr.6.2k
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Answer: C: Corrupt Database Error When Loading qvalue() Package
... Did you fully terminate your R/Rstudio session before restarting and issuing library("qvalue")?  Typically the R_decompress1 error occurs when inconsistent package images are in use/installed. http://stackoverflow.com/questions/10373098/error-in-fetchkey-internal-error-3-in-r-decompress1 ...
written 12 months ago by Vincent J. Carey, Jr.6.2k
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Comment: C: injectSNPS only for common variants
... MAF is a population-specific parameter.  You may be able to get some information out of AnnotationHub; I can't verify as I have a terrible connection at the moment. > query(ah, "Common SNPs") AnnotationHub with 3 records # snapshotDate(): 2016-10-11 # $dataprovider: UCSC # $species: Homo sapie ...
written 12 months ago by Vincent J. Carey, Jr.6.2k
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Comment: C: BiocParallel exporting function?
... You mean .parallel=TRUE, right?  I think it will be very hard to get advice on these questions without concise reproducible examples illustrating the concerns.  the .parallel parameter to dlply determines whether iteration will occur using foreach, and I believe there are ways to achieve the export ...
written 12 months ago by Vincent J. Carey, Jr.6.2k

Latest awards to Vincent J. Carey, Jr.

Scholar 19 months ago, created an answer that has been accepted. For A: How to get list of E.coli genes wit their details on Genome?
Scholar 20 months ago, created an answer that has been accepted. For A: How to get list of E.coli genes wit their details on Genome?
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For C: how can I install packages in docker/R/bioconductor so that they persist?
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