User: Todd Creasy

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Posts by Todd Creasy

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summarizeVariants from VariantAnnotation reordering genes in rownames
... When I use summarizeVariants with a GRangesList of genes, the genes are then reordered in the RangedSummarizedExperiment object and the assay(counts) values are incorrect. Is this a bug or can I control this reordering?   txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene genes <- genes(txd ...
variantannotation summarizevariants written 2.2 years ago by Todd Creasy0 • updated 2.1 years ago by Valerie Obenchain6.7k
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Comment: C: Can bplapply timeout when waiting for long jobs?
... Hi Martin, I think you're right. In fact, I'm already going down that path. Your code will be a big help in ironing this out. I'll post back here when I get something working.   -todd ...
written 3.5 years ago by Todd Creasy0
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Can bplapply timeout when waiting for long jobs?
... Hi, I'm writing some code to submit to a Torque cluster using BiocParallel. However, it appears that long running jobs do not "wait" and eventually throw an error (I've listed below). bplapply *does* submit to the cluster and I'm able to see the jobs via qstat and running on the node. However, it a ...
biocparallel written 3.5 years ago by Todd Creasy0 • updated 3.5 years ago by Martin Morgan ♦♦ 23k

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