User: roladali

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roladali20
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Posts by roladali

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Comment: C: DistanceToNearest() error: 'nLnode' and 'nRnode' must be single integers
... Thanks for the fix! ...
written 14 months ago by roladali20
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Answer: A: DistanceToNearest() error: 'nLnode' and 'nRnode' must be single integers
... I have figured out what triggers one of the errors but not the other: distanceToNearest(myRanges3, myRanges4, ignore.strand=T) Error in rep(seq(lx)[v], w) : invalid 'times' argument   seems to be triggered by ranges that start at 0. if I remove all the ranges that start at zero, the error is not ...
written 14 months ago by roladali20
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Comment: C: DistanceToNearest() error: 'nLnode' and 'nRnode' must be single integers
... I added the objects below.  Thanks! ...
written 14 months ago by roladali20
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Comment: C: DistanceToNearest() error: 'nLnode' and 'nRnode' must be single integers
... I added it below.  Is there another way to find the closest GRanges object besides distanceToNearest()? Thanks for the help! ...
written 14 months ago by roladali20
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Answer: A: DistanceToNearest() error: 'nLnode' and 'nRnode' must be single integers
... Hello, I am actually getting 2 different errors: > distanceToNearest(myRanges1, myRanges2, ignore.strand=T) Error in new_Hits(Class, from, to, nLnode, nRnode, mcols) :    'nLnode' and 'nRnode' must be single integers > distanceToNearest(myRanges3, myRanges4, ignore.strand=T) Error in rep(s ...
written 14 months ago by roladali20
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Comment: C: DistanceToNearest() error: 'nLnode' and 'nRnode' must be single integers
... biocLite isnt really updating the 8 packages   > biocLite() BioC_mirror: https://bioconductor.org Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.0 (2016-05-03). ...
written 14 months ago by roladali20
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Comment: C: DistanceToNearest() error: 'nLnode' and 'nRnode' must be single integers
... * Out-of-date packages Package BSgenome.Hsapiens.UCSC.hg19         "BSgenome.Hsapiens.UCSC.hg19"                  BSgenome.Hsapiens.UCSC.hg38        "BSgenome.Hsapiens.UCSC.hg38"                  DO.db                                        "DO.db"   IlluminaHumanMethylation450kanno.ilmn12.hg19 "Ill ...
written 14 months ago by roladali20
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Comment: C: DistanceToNearest() error: 'nLnode' and 'nRnode' must be single integers
... BiocInstaller::biocValid() * sessionInfo() R version 3.3.0 (2016-05-03) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.2 (Yosemite) locale: [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8 attached base packages: [1] stats4    parallel  stats     graphics ...
written 14 months ago by roladali20
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DistanceToNearest() error: 'nLnode' and 'nRnode' must be single integers
... I am trying to use distanceToNearest() to get the closest distance between two GRanges objects. The method usually works well but has been giving me an error (Error in new_Hits(Class, from, to, nLnode, nRnode, mcols) :    'nLnode' and 'nRnode' must be single integers) which I am not sure how to reso ...
genomicranges distancetonearest written 14 months ago by roladali20 • updated 14 months ago by Valerie Obenchain ♦♦ 6.4k
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TCGAbiolinks download error
... I am following the tutorial to use TCGAbiolinks to download expression and survival data but have not been able to download anything: Code: query <- TCGAquery(tumor = "brca", platform = "IlluminaHiSeq_RNASeqV2", level = "3") TCGAdownload(query, path = "../dataBrca", type = "rsem.genes.result ...
tcgabiolinks tcgadownload written 17 months ago by roladali20 • updated 16 months ago by tiagochst90

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