User: Peter Hickey
Peter Hickey • 330
- Reputation:
- 330
- Status:
- Trusted
- Location:
- Johns Hopkins University, Baltimore, USA
- Website:
- http://www.peterhickey...
- Twitter:
- PeteHaitch
- Scholar ID:
- Google Scholar Page
- Last seen:
- 2 weeks ago
- Joined:
- 5 years, 5 months ago
- Email:
- p***********@gmail.com
Posts by Peter Hickey
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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 4 weeks ago by
Peter Hickey • 330
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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 5 weeks ago by
Peter Hickey • 330
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... Thank you for including the code and sessionInfo() in your question, which makes it easy to help you.
Based on your sessionInfo(), you are mixing packages from different Bioconductor versions: minfi, minfiData, IlluminaHumanMethylation450kanno.ilmn12.hg19, and IlluminaHumanMethylation450kmanifest a ...
written 4 months ago by
Peter Hickey • 330
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Comment:
C: From RleList to RleArray
... Will try to write a PR to add this to DelayedArray over the next few days
...
written 5 months ago by
Peter Hickey • 330
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Answer:
A: From RleList to RleArray
... rm <- RleArray(unlist(rl), c(lengths(rl)[1], length(rl))) will give you what you want (the unlist() is cheap because of how an RleList is defined). With some checks added, this could become the as(rl, "RleArray") method.
...
written 5 months ago by
Peter Hickey • 330
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... Yes, it does sound a little odd. Especially since you have unstranded CpGs (my guess based on having 58,165,645 rows = 2 * 24 million CpGs in hg19)
...
written 5 months ago by
Peter Hickey • 330
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... That does sound unusual; smoothing is memory intensive but shouldn't be that bad. This is CpG methylation, correct? And you're running it with Meth.cov.fit <- BSmooth(Meth.cov, mc.cores = 32, verbose = TRUE)?
...
written 5 months ago by
Peter Hickey • 330
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... Hi Ravi,
I have seen this error before when running on a cluster with a large value of mc.cores. Unfortunately, I don't know the exact cause (I suspect one of the jobs dies, possibly because it runs out of memory).
I have been able to get around this by reducing to, say, mc.cores = 8. Does this wor ...
written 6 months ago by
Peter Hickey • 330
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Comment:
C: Error from scater package
... Please include the output of sessionInfo() in your question (http://www.bioconductor.org/help/support/posting-guide/)
...
written 6 months ago by
Peter Hickey • 330
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... Thanks for your patience, Alejandro. I've committed a fix - it's available from https://github.com/PeteHaitch/bsseq. If you're able to, would you please give it a try to confirm that it fixes the performance regression. It requires that you are using Bioc-devel and can then be installed with BiocIns ...
written 9 months ago by
Peter Hickey • 330
Latest awards to Peter Hickey
Scholar
10 months ago,
created an answer that has been accepted.
For A: t-statistic cutoff for finding DMRs with bsseq
Scholar
2.2 years ago,
created an answer that has been accepted.
For A: t-statistic cutoff for finding DMRs with bsseq
Scholar
2.2 years ago,
created an answer that has been accepted.
For A: t-statistic cutoff for finding DMRs with bsseq
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