User: Peter Hickey
Peter Hickey • 370
- Reputation:
- 370
- Status:
- Trusted
- Location:
- Johns Hopkins University, Baltimore, USA
- Website:
- http://www.peterhickey...
- Twitter:
- PeteHaitch
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- Google Scholar Page
- Last seen:
- 2 days, 23 hours ago
- Joined:
- 5 years, 7 months ago
- Email:
- p***********@gmail.com
Posts by Peter Hickey
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... Sharing my reply to Robert's email; he asked for the data behind a post I wrote that included a graph of number of packages per release (http://blog.revolutionanalytics.com/2015/08/a-short-introduction-to-bioconductor.html). The post is from a few releases back, but I've updated the code.
The data ...
written 19 days ago by
Peter Hickey • 370
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... Very good point re not clobbering result if invoked with se <- f(se, ...). Hmm, there are more dragons here than I'd initially considered. I'll keep thinking on this (it may be more trouble than it's worth). Thanks for your advice, Martin.
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written 20 days ago by
Peter Hickey • 370
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... Perhaps I need to think about this more. The design I had in mind is as follows.
f(): A user-level function that takes a SummarizedExperiment. It breaks up the assay-data into chunks and uses BiocParallel to process these chunks in parallel. Finally, it constructs a new assay from these outputs tha ...
written 21 days ago by
Peter Hickey • 370
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... In a long-running function I am writing, I use bptry() around bplapply() so that I might re-do failed tasks (this is such a cool feature!). If any failures are detected, I want to return a custom error message to help the user re-run just the failed tasks, along with the partial results. Right now, ...
written 23 days ago by
Peter Hickey • 370
• updated 22 days ago by
Martin Morgan ♦♦ 21k
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... That seems a reasonable request, Raymond. Let's continue the discussion on the GitHub issue (I prefer that for more code-focused issues).
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written 4 weeks ago by
Peter Hickey • 370
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... Thanks for the detailed bug report, @rcavalca. I can confirm that running 2B in a clean session leads to the error. However, it's not an issue with bsseq but rather something else, perhaps in SummarizedExpeirment. On BioC 3.7:
seqinfo_hg19 = GenomeInfoDb::Seqinfo(genome = 'hg19')
se <- Summarize ...
written 4 weeks ago by
Peter Hickey • 370
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... I was unable to replicate this on a Linux machine using Bioconductor 3.7.
Neither 'rngtools' or 'pkgmaker' appears to be archived on CRAN (as of 2018-05-14), although the CRAN check pages do indicate some errors on linux with r-devel, r-patched, and r-release (https://cran.r-project.org/web/checks/ ...
written 5 weeks ago by
Peter Hickey • 370
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... See above comment
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written 5 weeks ago by
Peter Hickey • 370
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... There's no general abind() method for DelayedArray at this time. However, for your particular example, you can achieve it with some trickery using aperm() with arbind():
suppressPackageStartupMessages(library(DelayedArray))
# NOTE: I add a 4th dimension to the array
a <- array(runif(1500000), ...
written 3 months ago by
Peter Hickey • 370
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... Please post your question separately rather than as a comment on an existing question. Your questions are very broad and I don't full understand where exactly you need help. Please read the posting guide so that others can help you more easily.
...
written 3 months ago by
Peter Hickey • 370
Latest awards to Peter Hickey
Popular Question
4 weeks ago,
created a question with more than 1,000 views.
For VariantAnnotation::readVcf is reordering the FORMAT field of my VCF file
Scholar
4 weeks ago,
created an answer that has been accepted.
For A: t-statistic cutoff for finding DMRs with bsseq
Scholar
11 months ago,
created an answer that has been accepted.
For A: About methylation data processing
Teacher
11 months ago,
created an answer with at least 3 up-votes.
For A: Error when generate mapToGenome
Scholar
11 months ago,
created an answer that has been accepted.
For A: t-statistic cutoff for finding DMRs with bsseq
Popular Question
11 months ago,
created a question with more than 1,000 views.
For Confusion over inconsistencies with showMethods('Rle') when loaded via GenomicRanges
Popular Question
11 months ago,
created a question with more than 1,000 views.
For Unable to load/install rtracklayer (v1.33.2) on OS X (possibly SSL-related?)
Scholar
12 months ago,
created an answer that has been accepted.
For A: t-statistic cutoff for finding DMRs with bsseq
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2.3 years ago,
created an answer that has been accepted.
For A: t-statistic cutoff for finding DMRs with bsseq
Scholar
2.3 years ago,
created an answer that has been accepted.
For A: t-statistic cutoff for finding DMRs with bsseq
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