User: enricoferrero

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enricoferrero560
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United Kingdom
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Posts by enricoferrero

<prev • 123 results • page 1 of 13 • next >
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Comment: C: Gviz IdeogramTrack fails with Error: failed to load HTTP resource
... This might be related to https://support.bioconductor.org/p/105322/ though the error message appears to be different. ...
written 19 days ago by enricoferrero560
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Gviz IdeogramTrack fails with Error: failed to load HTTP resource
... Hello, I get an HTTP connection error when using Gviz::IdeogramTrack(): library(Gviz) IdeogramTrack(genome="hg19", chromosome="chr7") Error: failed to load HTTP resource traceback() 18: stop(e) 17: (function (msg, code, domain, line, col, level, filename, class = "XMLError") { e = m ...
rtracklayer gviz http gviz-package written 19 days ago by enricoferrero560
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Comment: C: [VariantAnnotation] Preserve query metadata with locateVariants()
... Thanks Valerie, it works perfectly - not sure how I missed that column in the results object! ...
written 9 weeks ago by enricoferrero560
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[VariantAnnotation] Preserve query metadata with locateVariants()
... Is there any way to preserve the metadata in the query GRanges object when using locateVariants(query, subject, AllVariants()) from VariantAnnotation? Or is it possible to add the query metadata to the resulting GRanges? When calculating overlaps between two GRanges object I usually use findOverla ...
variantannotation metadata locatevariants mcols written 9 weeks ago by enricoferrero560 • updated 9 weeks ago by Valerie Obenchain ♦♦ 6.4k
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Answer: A: [gwascat] Updated GWAS catalog from file
... Based on Robert Castelo's answer below, I ended up doing this: download.file("http://www.ebi.ac.uk/gwas/api/search/downloads/alternative", destfile = "gwas_catalog_v1.0.1-associations_e90_r2017-12-04.tsv") snps <- read.delim("gwas_catalog_v1.0.1-associations_e90_r2017-12-04.tsv", check.names = ...
written 9 weeks ago by enricoferrero560
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Comment: C: [gwascat] Updated GWAS catalog from file
... Thanks. Yes, this would probably work but it's not very elegant - especially considering this is training material for students. I wonder wheter it would not be easier and more straightforward to follow to simply create a GRanges object at that point? ...
written 9 weeks ago by enricoferrero560
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[gwascat] Updated GWAS catalog from file
... Hello, Is there any way to get an up-to-date version of the GWAS catalog starting from an existing file? Currently the version accessible with data(ebicat38) is outdated (January 2016) and the function makeCurrentGwascat() only accepts a URL as argument, not an existing file. I'm preparing some tr ...
gwascat written 9 weeks ago by enricoferrero560
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Comment: C: keys() fails on EnsDb.Hsapiens.v75 on Bioc 3.5
... Yep, this solves it, thank you. Feel free to add it as an answer so I can accept it. ...
written 9 months ago by enricoferrero560
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Comment: C: keys() fails on EnsDb.Hsapiens.v75 on Bioc 3.5
... This is cool but, is there a way to grab the EnsDb object without having to look up its name in the AnnotationHub (i.e.:  AH53211)? BTW, I didn't mean to hijack my own thread : i still get that error when trying to access the EnsDb objects with keys() or genes(). ...
written 9 months ago by enricoferrero560
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Comment: C: keys() fails on EnsDb.Hsapiens.v75 on Bioc 3.5
... Also, I get the same error when using genes(EnsDb.Hsapiens.v75, columns = "gene_id")$gene_id ...
written 9 months ago by enricoferrero560

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Student 10 months ago, asked a question with at least 3 up-votes. For Can't upgrade to Bioconductor 3.3?
Popular Question 10 months ago, created a question with more than 1,000 views. For biomaRt proxy issues
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Scholar 22 months ago, created an answer that has been accepted. For A: How to correctly import Bismark coverage files into bsseq?
Popular Question 22 months ago, created a question with more than 1,000 views. For Linkage disequilibrium with 1000 Genomes/HapMap
Popular Question 22 months ago, created a question with more than 1,000 views. For How to properly sort GRanges?
Popular Question 22 months ago, created a question with more than 1,000 views. For Simple pathway enrichment analysis for gene lists
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Scholar 22 months ago, created an answer that has been accepted. For A: How to correctly import Bismark coverage files into bsseq?
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