User: dan.gatti

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dan.gatti0
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Posts by dan.gatti

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BiocParallel and variable scope in child processes
... I would like to call a function that parallelizes the computation and I'd like to use FORK clusters so that I don't have to export the variables I'm operating on to each cluster.  I've made a minimal toy example. The following code works fine. All of the clusters can see the variable 'a': library( ...
biocparallel parallel variable scope fork written 12 months ago by dan.gatti0 • updated 12 months ago by Martin Morgan ♦♦ 20k
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Answer: A: BiocInstaller_1.16.5.zip not found when using biocLite("BiocUpgrade")
... That worked.  Awesome.  Thanks. ...
written 18 months ago by dan.gatti0
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BiocInstaller_1.16.5.zip not found when using biocLite("BiocUpgrade")
... I just installed R 3.3 and was trying to upgrade my Bioconductor packages. But I ran into an odd "404 file not found" error with the BiocInstaller file. > source("http://bioconductor.org/biocLite.R") Bioconductor version 2.14 (BiocInstaller 1.14.3), ?biocLite for help A newer version of Biocond ...
bioclite biocupgrade written 18 months ago by dan.gatti0 • updated 18 months ago by Martin Morgan ♦♦ 20k
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Answer: A: VariantAnnotation: scanVcfHeader() throws error about missing keepNA
... Yes, it's definitely reproducible.  However, I uninstalled R and Rtools and installed R 3.2.1 and Rtools 3.2.  Then I updated all of my Bioconductor packages and now the bug is gone.  Sorry for the false alarm. I didn't think that the minor R 3.2.1 release would make a difference. ...
written 2.4 years ago by dan.gatti0
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VariantAnnotation: scanVcfHeader() throws error about missing keepNA
... Not sure what happened. This works in R 3.1.1 with VariantAnnotation_1.12.9. I'm getting an error that says that "keepNA" is missing when reading the header for this VCF file. > library(VariantAnnotation) > snpfile = "ftp://ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/mgp.v5.merged.snps_all.db ...
variantannotation readvcfheader written 2.4 years ago by dan.gatti0
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Producing alternate protein sequences from VCF
... I have a VCF with SNPs for several strains of mice. I would like to extract the nonsynonymous SNPs and create alternate peptide sequences for each strain. I can do this by hand with several lines of code, but I'm wondering if there is a pipeline or a package that can do this?  The functionality woul ...
vcf protein written 2.6 years ago by dan.gatti0
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Answer: A: Converting a DNAStringSetList to characters quickly
... Good point. I looked at the 0.04 and 0.01 and misinterpreted them. Thanks for the clarification.   ...
written 2.6 years ago by dan.gatti0
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Answer: A: Converting a DNAStringSetList to characters quickly
... Thanks. The CharacterList is a new class for me. I need to write out a table with polymorphic SNPs in a subset of the strains from the VCF. And they need to be coded as 0 or 1. Otherwise, I'd use writeVcf(). Just to close out the question for others, I performed a few timing runs. The last two meth ...
written 2.6 years ago by dan.gatti0
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Converting a DNAStringSetList to characters quickly
... I'm using read.vcf() in the VariantAnnotation package to get SNPs from a VCF file. It returns a CollapsedVCF object. I then extract the alternate allele calls using fixed(vcf)$ALT, which returns a DNAStringSetList. Each element contains a DNAStringSet with one or more characters (there are tri-morph ...

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