User: Peter Hickey

gravatar for Peter Hickey
Peter Hickey370
Reputation:
370
Status:
Trusted
Location:
Johns Hopkins University, Baltimore, USA
Website:
http://www.peterhickey...
Twitter:
PeteHaitch
Scholar ID:
Google Scholar Page
Last seen:
2 days, 23 hours ago
Joined:
5 years, 7 months ago
Email:
p***********@gmail.com

Posts by Peter Hickey

<prev • 75 results • page 1 of 8 • next >
0
votes
3
answers
62
views
3
answers
Answer: A: How to obtain summary statistics for all Bioc releases
... 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 Hickey370
0
votes
1
answers
56
views
1
answers
Comment: C: Help using 'handler' function with bptry()
... 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. ...
written 20 days ago by Peter Hickey370
0
votes
1
answers
56
views
1
answers
Comment: C: Help using 'handler' function with bptry()
... 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 Hickey370
1
vote
1
answer
56
views
1
answer
Help using 'handler' function with bptry()
... 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, ...
biocparallel error handling written 23 days ago by Peter Hickey370 • updated 22 days ago by Martin Morgan ♦♦ 21k
0
votes
1
answers
66
views
1
answers
Answer: A: Request to remove requirement for gr to have widths 1 in BSseq constructor
... That seems a reasonable request, Raymond. Let's continue the discussion on the GitHub issue (I prefer that for more code-focused issues).  ...
written 4 weeks ago by Peter Hickey370
0
votes
1
answers
77
views
1
answers
Comment: C: Strange error in bsseq when trying to assign seqinfo
... 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 Hickey370
0
votes
1
answers
68
views
1
answers
Comment: C: Dependency installation error due to no longer available CRAN packages ('rngtool
... 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 Hickey370
0
votes
1
answers
68
views
1
answers
Answer: A: Dependency installation error due to no longer available CRAN packages ('rngtool
... See above comment ...
written 5 weeks ago by Peter Hickey370
0
votes
1
answers
94
views
1
answers
Answer: A: how to combine multiple DelayedArray to a high dimension array
... 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 Hickey370
0
votes
3
answers
525
views
3
answers
Comment: C: Finding DMRs using dmrFinder in bsseq
... 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 Hickey370

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
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: From RleList to RleArray
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
Scholar 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

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 430 users visited in the last hour