User: Charles Plessy

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30
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New User
Location:
Japan
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1 day, 14 hours ago
Joined:
2 years, 7 months ago
Email:
c***********@plessy.org

Posts by Charles Plessy

<prev • 22 results • page 1 of 3 • next >
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Build error: could not find function "bplapply"
... The current version (1.21.4) of the CAGEr package fails to check with the following error: * checking examples ... ERROR Running examples in ‘CAGEr-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: CustomConsensusClusters & ...
biocparallel build report written 6 days ago by Charles Plessy30 • updated 6 days ago by Martin Morgan ♦♦ 21k
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Comment: C: What is the proper way to modify mcols of a GRanges inside a GRangesList?
... As of today, I do not manage to reproduce the examples above.  After running example("GRangesList") to create a grl object with "score" and "GC" mcols, here is what I get: > grl[,"newColumn"] <- "new value" Error in `[<-`(`*tmp*`, , "newColumn", value = "new value") : replacement value ...
written 11 days ago by Charles Plessy30
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Circular plot of transcript models with ggbio.
... Hello, ggbio is great to plot transcript models, and great to plot features on circular genomes, but I could not find a way to plot transcript models on a circular genome. Is it unsupported at the moment ? Thanks a lot for this brilliant package. ! Charles ...
ggbio written 11 weeks ago by Charles Plessy30
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Answer: A: clusterCTSS() error when running CAGEr
... Thanks for the report. On a virtual machine running R 3.2.3, I tried the following test, which worked; load(system.file("data", "exampleCAGEset.RData", package="CAGEr")) clusterCTSS(object = exampleCAGEset, method = "paraclu") Then I tried after normalisation and it did not work anymore. load(s ...
written 3 months ago by Charles Plessy30
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Comment: C: bplapply slow to decide number of cores
... Indeed the speed has a lot to do with the session. I tried the bplapply command in a fresh session and it took 0.6 s.  Then I loaded GenomicRanges and it took 1.4 s, then I added SummarizedExperiment, MultiAssayExperiment and rtracklayer,  and the elapsed time rose to 2.0, 2.3 and 2.8 s respectively ...
written 3 months ago by Charles Plessy30
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bplapply slow to decide number of cores
... I am surprised that bplapply() takes a few seconds to detect the number of available cores, while multicoreWorkers() or MulticoreParam() are fast when they run by themselves: > system.time(BiocParallel::bplapply(1:1e2 , function(x) order(rnorm(n=1e3)), BPPARAM = MulticoreParam())) user syst ...
biocparallel written 3 months ago by Charles Plessy30 • updated 3 months ago by Martin Morgan ♦♦ 21k
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Comment: C: Generic functions for DataFrames of Rle objects ?
... Thanks a lot Hervé! It took me some time to understand the obvious, but the DelayedArray wrappers are exactly what I needed. Would you recommend to I wrap in DelayedArrays just before performing matrix-like operations, or to use the DelayedArray class as the base class for the assays in the Summari ...
written 5 months ago by Charles Plessy30
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Answer: A: CAGEr BAM files size issue
... I have pushed update 1.18.1 to the [Bioconductor release 3.5 branch](http://bioconductor.org/packages/3.5/bioc/html/CAGEr.html), where I [implemented the solution discussed above](https://github.com/Bioconductor-mirror/CAGEr/commit/0a1c85d2e8f99b0104446fb301f013ce2b4dfaad) (parse the qualities by ch ...
written 5 months ago by Charles Plessy30
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Comment: C: CAGEr BAM files size issue
... Hi Hervé and Magda, thanks for the report and the guidance. getCTSS() loads the BAM files with Rsamtools::ScanBam, and then extracts the qualities from the returned object, in which they are stored as a PhredQuality object. For each read, an average quality is calculated, and that requires the Phr ...
written 5 months ago by Charles Plessy30
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Comment: A: CAGEr BAM files size issue
... Dear Magda, thanks for the report; could you suggest a pair of publicly available BAM files where one triggers the bug and the other does not ? ...
written 6 months ago by Charles Plessy30

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