Moderator: Vincent J. Carey, Jr.

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Posts by Vincent J. Carey, Jr.

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Comment: C: VariantAnnotation error with readVcf after genotypeToSnpMatrix
... I can't reproduce on several platforms.  Some of your packages seem out of date.  Use library(BiocInstaller); biocValid() and update to a consistent state.  I don't see VariantAnnotation version in your sessionInfo() above. ...
written 8 weeks ago by Vincent J. Carey, Jr.6.1k
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Answer: C: Corrupt Database Error When Loading qvalue() Package
... Did you fully terminate your R/Rstudio session before restarting and issuing library("qvalue")?  Typically the R_decompress1 error occurs when inconsistent package images are in use/installed. http://stackoverflow.com/questions/10373098/error-in-fetchkey-internal-error-3-in-r-decompress1 ...
written 8 weeks ago by Vincent J. Carey, Jr.6.1k
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Comment: C: injectSNPS only for common variants
... MAF is a population-specific parameter.  You may be able to get some information out of AnnotationHub; I can't verify as I have a terrible connection at the moment. > query(ah, "Common SNPs") AnnotationHub with 3 records # snapshotDate(): 2016-10-11 # $dataprovider: UCSC # $species: Homo sapie ...
written 10 weeks ago by Vincent J. Carey, Jr.6.1k
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Comment: C: BiocParallel exporting function?
... You mean .parallel=TRUE, right?  I think it will be very hard to get advice on these questions without concise reproducible examples illustrating the concerns.  the .parallel parameter to dlply determines whether iteration will occur using foreach, and I believe there are ways to achieve the export ...
written 10 weeks ago by Vincent J. Carey, Jr.6.1k
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Answer: A: Use of org.Hs.eg.db and TxDb.Hsapiens.UCSC.hg19.knownGene
... You can get information about the sources of the annotation resources by mentioning them. > TxDb.Hsapiens.UCSC.hg19.knownGene TxDb object: # Db type: TxDb # Supporting package: GenomicFeatures # Data source: UCSC # Genome: hg19 # Organism: Homo sapiens # Taxonomy ID: 9606 # UCSC Table: knownGe ...
written 10 weeks ago by Vincent J. Carey, Jr.6.1k
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Comment: C: pd.hta.2.0 oddity, possible RSQLite bug?
... thanks Jim and Martin -- this has been very helpful. On Wed, Sep 14, 2016 at 4:48 PM, Martin Morgan [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Martin Morgan <https: support.bioconductor.org="" u="" 1513="" ...
written 4 months ago by Vincent J. Carey, Jr.6.1k
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pd.hta.2.0 oddity, possible RSQLite bug?
... I am finding that there is some loss of information when using high- vs. low-level DBI to get annotation from a pd.hta.2.0 sqlite database. low level approach yields details on 'transcript_cluster_id" > pd.hta.2.0 Class........: AffyHTAPDInfo Manufacturer.: Genome Build.: The Genome Build ...
oligo rsqlite pd.hta.2.0 written 4 months ago by Vincent J. Carey, Jr.6.1k • updated 4 months ago by James W. MacDonald41k
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Comment: C: RBGL installation error
... The devel branch of RBGL now employs an excerpt from boost 1.61.0 On two linux systems it passes check in R 3.3.0 with a warning about abort() in two of the boost functions I cannot get it to build with el capitan clang++ ... let's see how the build system does.   All that was needed to get compa ...
written 5 months ago by Vincent J. Carey, Jr.6.1k
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Comment: C: RBGL installation error
... With boost 1.61, the following RBGL programs trigger errors like those noted above bbc.cpp  dominatorTree.cpp  ordering.cpp  planar.cpp  shortestPath.cpp There are also problems with some of the functions in interfaces.cpp.  A nontrivial fraction of the procedures compile with boost 1.61.  If we ...
written 5 months ago by Vincent J. Carey, Jr.6.1k
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Comment: C: Fusion gene mutation detection
... have you read the vignette for the "chimera" package?   http://bioconductor.org/packages/release/bioc/html/chimera.html ...
written 5 months ago by Vincent J. Carey, Jr.6.1k

Latest awards to Vincent J. Carey, Jr.

Scholar 10 months ago, created an answer that has been accepted. For A: How to get list of E.coli genes wit their details on Genome?
Teacher 14 months ago, created an answer with at least 3 up-votes. For C: how can I install packages in docker/R/bioconductor so that they persist?
Centurion 2.4 years ago, created 100 posts.

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