User: Peter Hickey

gravatar for Peter Hickey
Peter Hickey240
Reputation:
240
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Trusted
Location:
Australia
Website:
http://www.peterhickey...
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PeteHaitch
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Google Scholar Page
Last seen:
4 days, 15 hours ago
Joined:
4 years, 10 months ago
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Posts by Peter Hickey

<prev • 58 results • page 1 of 6 • next >
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Answer: A: Unusually long running times for getMeth function since latest release
... 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 Hickey240
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Comment: C: Unusually long running times for getMeth function since latest release
... 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 Hickey240
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Comment: C: Unusually long running times for getMeth function since latest release
... 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 Hickey240
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Comment: C: Error in loading GenomicMethylSet: "no slot of name 'elementMetadata' for this o
... 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 Hickey240
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Comment: C: Finding DMRs using dmrFinder in bsseq
... 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 Hickey240
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Answer: A: bsseq combineList: how to get an HDF5Array-backed object as return value?
... 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 Hickey240
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Comment: C: Finding DMRs using dmrFinder in bsseq
... 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 Hickey240
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Comment: C: Finding DMRs using dmrFinder in bsseq
... 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 Hickey240
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Comment: C: Finding DMRs using dmrFinder in bsseq
... 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 Hickey240
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Comment: C: Finding DMRs using dmrFinder in bsseq
... 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 Hickey240

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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