User: Peter Hickey
Peter Hickey • 240
- Reputation:
- 240
- Status:
- Trusted
- Location:
- Australia
- Website:
- http://www.peterhickey...
- Twitter:
- PeteHaitch
- Scholar ID:
- Google Scholar Page
- Last seen:
- 4 days, 15 hours ago
- Joined:
- 4 years, 10 months ago
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Posts by Peter Hickey
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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 7 weeks ago by
Peter Hickey • 240
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... Hi Alejandro,
Reproducible code and data would be appreciated. No need for it to be the
full object, just enough for issue to be a noticeable drag on performance.
Cheers,
Pete
On Fri., 30 Jun. 2017, 9:37 am Alejandro Reyes [bioc], <
noreply@bioconductor.org> wrote:
> Activity on a post ...
written 7 weeks ago by
Peter Hickey • 240
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... I noticed this too but haven't had time to fix. I have an inkling of what's
causing this and I'll try to fix over the weekend
On Thu., 29 Jun. 2017, 5:48 pm Kasper Daniel Hansen [bioc], <
noreply@bioconductor.org> wrote:
> Activity on a post you are following on support.bioconductor.org
& ...
written 7 weeks ago by
Peter Hickey • 240
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... Please include the result of running sessionInfo() to help diagnose the problem. Does it work if you load the object from command line R rather than from Rstudio?
...
written 7 weeks ago by
Peter Hickey • 240
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... There were multiple warnings following bsseq.data.smoothed <- BSmooth(bsseq.data, verbose=TRUE). Did you look to see what there were? Above I suggested that because you are analysing RRBS data you would need to explore different parameters to BSmooth() but you've used the defaults. I suspect this ...
written 9 weeks ago by
Peter Hickey • 240
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... Hi Martin,
combineList(hdf5_BS1, hdf5_BS2, BACKEND = "HDF5Array") will give you a HDF5Array-backed BSseq object. It's somewhat buried in the docs, but see ?combineList.
Currently, the default location for HDF5 files is specified via HDF5Array::setHDF5DumpDir(). You can check the current dump dir ...
written 11 weeks ago by
Peter Hickey • 240
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... I am unable to reproduce the error. However, your example code has a bug: list.files(pattern="*.cov") -> cov.files means that the chr16 and chr20 data will be considered to have come from separate samples. This is not what you want.
I tidied up and simplified your example code and was able to su ...
written 3 months ago by
Peter Hickey • 240
0
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242
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... Thanks, Nastasia. Can you please also post the exact command you ran that worked for chr20 but not for chr16
...
written 3 months ago by
Peter Hickey • 240
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... It's difficult to know what's causing the error from that output. Are you able to share the chr16 data with me (e.g., via Dropbox)? I could then investigate further
...
written 3 months ago by
Peter Hickey • 240
0
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242
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... 1. Setting ns so large is probably not a good idea for RRBS data. As documented, ns is the minimum number of methylation loci in a smooth window. Most RRBS captured regions will contain many, many fewer CpGs, so you will be smoothing over large windows containing several clusters of CpGs with large ...
written 3 months ago by
Peter Hickey • 240
Latest awards to Peter Hickey
Scholar
10 weeks ago,
created an answer that has been accepted.
For A: t-statistic cutoff for finding DMRs with bsseq
Scholar
18 months ago,
created an answer that has been accepted.
For A: t-statistic cutoff for finding DMRs with bsseq
Scholar
18 months ago,
created an answer that has been accepted.
For A: t-statistic cutoff for finding DMRs with bsseq
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