User: enricoferrero

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enricoferrero570
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Switzerland
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Posts by enricoferrero

<prev • 126 results • page 1 of 13 • next >
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Comment: C: [limma] Define contrasts for model with covariates
... Thanks Gordon!  Can you please explain why that's the case? I.e.: why only the first categorical variable in the formula gets both levels as coefficients? ...
written 7 weeks ago by enricoferrero570
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[limma] Define contrasts for model with covariates
... I'm having a hard time understanding how to pull out the relevant contrasts when using a model with covariates in limma. Let's say I have the following gene expression matrix and experimental variables: library(limma) set.seed(16) mat <- matrix(rnorm(600), 100, 6) age <- c(45, 55, 47, 56, ...
limma model.matrix makecontrasts written 7 weeks ago by enricoferrero570 • updated 7 weeks ago by Gordon Smyth34k
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Comment: C: Invitation to submit articles to the Bioconductor gateway on F1000Research
... I have a cross-package workflow which was approved by referees a few weeks ago: https://f1000research.com/articles/7-121/v2 I would love for it to be part of BioC 2018 - is that possible even if it was published before the call? ...
written 4 months ago by enricoferrero570
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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 6 months ago by enricoferrero570
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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 6 months ago by enricoferrero570
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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 8 months ago by enricoferrero570
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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 8 months ago by enricoferrero570 • updated 8 months ago by Valerie Obenchain ♦♦ 6.5k
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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 8 months ago by enricoferrero570
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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 8 months ago by enricoferrero570
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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 8 months ago by enricoferrero570

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Great Question 11 weeks ago, created a question with more than 5,000 views. For [GenomicRanges] subsetByOverlaps to keep info from both GRanges objects?
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Linkage disequilibrium with 1000 Genomes/HapMap
Popular Question 11 weeks ago, created a question with more than 1,000 views. For biomaRt proxy issues
Popular Question 15 months ago, created a question with more than 1,000 views. For How to properly sort GRanges?
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Scholar 15 months ago, created an answer that has been accepted. For A: How to correctly import Bismark coverage files into bsseq?
Popular Question 15 months ago, created a question with more than 1,000 views. For Simple pathway enrichment analysis for gene lists
Great Question 15 months ago, created a question with more than 5,000 views. For How to properly sort GRanges?
Great Question 15 months ago, created a question with more than 5,000 views. For [GenomicRanges] subsetByOverlaps to keep info from both GRanges objects?
Popular Question 16 months ago, created a question with more than 1,000 views. For biomaRt proxy issues
Student 16 months ago, asked a question with at least 3 up-votes. For Can't upgrade to Bioconductor 3.3?
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Scholar 2.3 years ago, created an answer that has been accepted. For A: How to correctly import Bismark coverage files into bsseq?
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Popular Question 2.3 years ago, created a question with more than 1,000 views. For Linkage disequilibrium with 1000 Genomes/HapMap
Popular Question 2.3 years ago, created a question with more than 1,000 views. For How to properly sort GRanges?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Simple pathway enrichment analysis for gene lists
Popular Question 2.3 years ago, created a question with more than 1,000 views. For [DESeq2] Cook's distance flagging for continuous variables
Scholar 2.3 years ago, created an answer that has been accepted. For A: How to correctly import Bismark coverage files into bsseq?
Popular Question 2.5 years ago, created a question with more than 1,000 views. For biomaRt no longer works with proxy after upgrade
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Scholar 2.7 years ago, created an answer that has been accepted. For A: How to correctly import Bismark coverage files into bsseq?
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