User: Peter Hickey
Peter Hickey • 440
- Reputation:
- 440
- Status:
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- Location:
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Website:
- http://www.peterhickey...
- Twitter:
- PeteHaitch
- Scholar ID:
- Google Scholar Page
- Last seen:
- 1 week, 4 days ago
- Joined:
- 6 years, 1 month ago
- Email:
- p***********@gmail.com
Posts by Peter Hickey
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... Using `normalizePath()` worked. Thanks, Henrik! ...
written 14 days ago by
Peter Hickey • 440
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... I think this means TDFUtils exists in the .jar file, but I'm pretty outside my knowledge here.
$ jar tf ~/miniconda3/share/igvtools-2.3.93-0/igvtools.jar | grep TDFUtils
org/broad/igv/tdf/TDFUtils.class
...
written 14 days ago by
Peter Hickey • 440
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... Do you know if this trick still works, Henrik? I can't get it working on my machine but the combination of rJava, a conda-installed igvtools, and an the general lack of documentation on TDF makes me unsure where the fault lies.
library(rJava)
.jinit(classpath="~/miniconda3/share/igvtools-2.3.93-0/i ...
written 14 days ago by
Peter Hickey • 440
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Why is it beneficial to store the data as a single Rle in SolidRleArraySeed?
I think it's more the case that this is a simpler object to design and program with (Hervé Pagès will know best).
Doesn't that limit to the total size of the matrix since it spans all columns?
Yes, I think so.
If yo ...
written 6 weeks ago by
Peter Hickey • 440
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... suppressPackageStartupMessages(library(S4Vectors))
suppressPackageStartupMessages(library(DelayedArray))
nrow <- 200L
ncol <- 5L
# Generate some data that can be efficiently run length encoded.
x <- Rle(500L + sort(rpois(nrow * ncol, 10)))
x
#> integer-Rle of length 1000 with 21 runs
# ...
written 6 weeks ago by
Peter Hickey • 440
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... I'm going to assume we're talking about representing 2-dimesionsal arrays.
It comes down to how the data are stored (i.e. run length encoded):
A DataFrame with Rle columns is run length encoded column-wise with a separate Rle per column.
A SolidRleArraySeed-backed DelayedArray is run length enc ...
written 6 weeks ago by
Peter Hickey • 440
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... Thanks, Aaron. Very helpful (as always).
...
written 7 weeks ago by
Peter Hickey • 440
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... I've got an experiment with eight 10x scRNA-seq runs that I'm analysing by starting with something based on the simpleSingleCell workflow. I constructed each SingleCellExperiment with DropletUtils::read10xCounts().
I'm looking for any opinions or advice on when to combine these into one SingleCellE ...
written 7 weeks ago by
Peter Hickey • 440
• updated 7 weeks ago by
Aaron Lun • 21k
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... I believe this is cross-posted from https://github.com/hansenlab/minfi/issues/173. Based on the sessionInfo() you posted there, you are using an old version of minfi. As recommended in http://www.bioconductor.org/help/support/posting-guide/, please try updating to the latest version (see http://www. ...
written 3 months ago by
Peter Hickey • 440
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... Please include the output of sessionInfo() otherwise we don't know what version of R or minfi you are using. Please also read http://www.bioconductor.org/help/support/posting-guide/ for advice on creating a question that will be easier for people to help you answer.
...
written 3 months ago by
Peter Hickey • 440
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For A: t-statistic cutoff for finding DMRs with bsseq
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For VariantAnnotation::readVcf is reordering the FORMAT field of my VCF file
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For A: t-statistic cutoff for finding DMRs with bsseq
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For VariantAnnotation::readVcf is reordering the FORMAT field of my VCF file
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For Confusion over inconsistencies with showMethods('Rle') when loaded via GenomicRanges
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For A: About methylation data processing
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For A: t-statistic cutoff for finding DMRs with bsseq
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For A: t-statistic cutoff for finding DMRs with bsseq
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For A: t-statistic cutoff for finding DMRs with bsseq
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For A: t-statistic cutoff for finding DMRs with bsseq
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