User: Kipper Fletez-Brant

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Posts by Kipper Fletez-Brant

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Comment: C: flowClean error argument is of length zero
... Great, glad to hear it! On Thu, Oct 5, 2017 at 10:14 AM, simeen.malik [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User simeen.malik <https: support.bioconductor.org="" u="" 14102=""/> wrote Comment: > flow ...
written 6 weeks ago by Kipper Fletez-Brant140
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Comment: C: flowClean error argument is of length zero
... OK, you are on v 1.12. I think you should upgrade to v 1.16, which is currently on Bioconductor release, as there are some bug fixes that may/may not take of your problem. One other thing I've seen is that occasionally the time parameter is for some reason constant for a subset of the data (i.e. t ...
written 6 weeks ago by Kipper Fletez-Brant140
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Answer: A: flowClean error argument is of length zero
... Hi Simeen, Can you post your sessionInfo()? On Wed, Oct 4, 2017 at 3:34 AM, simeen.malik [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User simeen.malik <https: support.bioconductor.org="" u="" 14102=""/> wrot ...
written 6 weeks ago by Kipper Fletez-Brant140
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Comment: C: Could not find function "new:
... It's especially weird, given that the build reports are coming up OK (https://www.bioconductor.org/checkResults/3.4/bioc-20170415/#F) ...
written 4 months ago by Kipper Fletez-Brant140
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Comment: C: Could not find function "new:
... This is very strange and should not be happening.  I'll look into this. ...
written 4 months ago by Kipper Fletez-Brant140
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Contradictory Messages from rhdf5
... Hi, I'm trying to create an HDF5 file using the `rhdf5` library.  However, it seems that either I cannot create general attributes for the file, or there is some confusion about what I am doing, as `rhdf5` both can and cannot generate the attribute.  Here is a minimal example:   tmp <- "tmp.h ...
rhdf5 hdf5 written 6 months ago by Kipper Fletez-Brant140 • updated 3 months ago by Mike Smith2.1k
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Comment: C: Best way to import from multiple VCF files?
... Hmm... re: devel, I suppose I am not using it.  Will try that specifically.  As far the GRObject goes: library(AnnotationHub) ah <- subset(AnnotationHub(), species == "Homo sapiens") qhs <- query(query(ah, "CTCF"), "GM12878") ctcf <- subset(qhs, title == "wgEncodeAwgTfbsUwGm12878CtcfUniPk ...
written 15 months ago by Kipper Fletez-Brant140
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Comment: C: Best way to import from multiple VCF files?
... I am working with the VcfStack/RangedVcfStack ideas now ... I just wanted to point out a discrepancy between the docs and the current package: The following: slens <- seqlengths(BSgenome.Hsapiens.UCSC.hg19)[1:24] slens <- Seqinfo(seqnames=names(slens), seqlengths=slens, genome="hg19") names ...
written 15 months ago by Kipper Fletez-Brant140
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Comment: C: Best way to import from multiple VCF files?
... I am marking your answer as correct bc it pointed me in the right direction - embarrassingly the VCF files are all under the NCBI format for chr names, while my GRanges object was using the UCSC format  :( Nonetheless, I have benefitted from this discussion, as I was wholly unaware of VcfStack and ...
written 15 months ago by Kipper Fletez-Brant140
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Comment: C: Best way to import from multiple VCF files?
... Good point about TabixFileLIst: tab <- TabixFileList(vcf.fl, index=paste(vcf.fl, "tbi", sep=".")) ## vcf.fl is the same as above However, when I try your suggestion, I get the following:   vcf.rng <- readVcf(tab[[1]], "hg19", param=ctcf) Error: scanVcf: scanVcf: scanTabix: 'chr1' not pre ...
written 15 months ago by Kipper Fletez-Brant140

Latest awards to Kipper Fletez-Brant

Scholar 2.8 years ago, created an answer that has been accepted. For A: Programmatic use of flowQ?

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