Moderator: Vincent J. Carey, Jr.

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Posts by Vincent J. Carey, Jr.

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Answer: A: No annotation for single SNPs
... "according to the UCSC the SNP is part of an intron" -- but you have used AllVariants(promoter=PromoterVariants(downstream=500))) in your locateVariants() call.  Try IntronVariants().  I would not be surprised if there were still some mismatches -- please provide full details if identified, it i ...
written 8 months ago by Vincent J. Carey, Jr.6.2k
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Comment: C: Using AMI with StarCluster - error authenticating
... We are finding that cfncluster creation of clusters in EC2 is extremely slow, relative to the solution available a few years through starcluster.  Any other approaches in use in our community? ...
written 11 months ago by Vincent J. Carey, Jr.6.2k
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Comment: C: How to render summary list for `GRangesList` by using `SummarizedExperiment` pac
... I don't know that SummarizedExperiment is a good target for what you are trying to do. Is there a matrix of values to serve as "assay", with rows corresponding to features and columns corresponding to samples? Organizing such a matrix in coordination with feature-level and sample-level and experime ...
written 11 months ago by Vincent J. Carey, Jr.6.2k
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Comment: C: How to render summary list for `GRangesList` by using `SummarizedExperiment` pac
...   Briefly, there is no simple approach to this.  However, to get a working example: library(GenomicRanges) library(SummarizedExperiment) example(GRangesList) # creates 'grl' in .GlobalEnv colrep = function(x,n) matrix(x, nr=length(x), nc=n) # utility to create usable 'assay' msel = lapply(grl, ...
written 11 months ago by Vincent J. Carey, Jr.6.2k
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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 12 months ago by Vincent J. Carey, Jr.6.2k
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Comment: C: "developing" with HDF5Array
... Excellent.  Thanks very much. ...
written 12 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 12 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 12 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 12 months ago by Vincent J. Carey, Jr.6.2k

Latest awards to Vincent J. Carey, Jr.

Scholar 22 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 23 months ago, created an answer that has been accepted. For A: How to get list of E.coli genes wit their details on Genome?
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