User: Sigve Nakken

gravatar for Sigve Nakken
Sigve Nakken • 50
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50
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Location:
Norway
Last seen:
3 years, 6 months ago
Joined:
5 years, 6 months ago
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s*****@ifi.uio.no

Posts by Sigve Nakken

<prev • 7 results • page 1 of 1 • next >
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ENSEMBL_MART_FUNCGEN not accessible through biomaRt?
... Hi, I am trying to access the Ensembl Regulatory Build through the biomaRt package, using the following commands: ensembl_mart <- biomaRt::useMart(“ENSEMBL_MART_FUNCGEN") ensembl_mart <- biomaRt::useDataset(“hsapiens_regulatory_feature", mart = ensembl_mart) queryAttributes <- c('regul ...
biomart ensemble mart ensembldb regulatory written 3.5 years ago by Sigve Nakken • 50 • updated 3.5 years ago by Thomas Maurel • 770
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Answer: A: readVcfAsVRanges + FilterRules
... Hi Valerie, Thanks for the rapid response! Processing one sample at a time, using samples in readVcfAsVRanges, appears to be the approach that works for me. I tried the tabix-approach too, but that one gave strange results (not sure why). I understand the row-based filtering logic used in filterVc ...
written 4.8 years ago by Sigve Nakken • 50
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readVcfAsVRanges + FilterRules
... Hi, I have successfully used the VariantAnnotation (1.12.9 now) for processing my multi-sample VCF files for some time now. Especially, I have utilized the combination of filterVcf (with prefilters) and readVcfAsVRanges to retrieve sample variant calls from my sequencing projects. I have not been a ...
variantannotation readvcfasvranges filtervcf filterrules written 4.8 years ago by Sigve Nakken • 50 • updated 4.8 years ago by Martin Morgan ♦♦ 24k
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VCF class: different length when unlisting INFO CompressedCharacterList
... How do I access the ID column of the VCF when using readVcfAsVranges? I cannot seem to find these values in the resulting VRanges object. best, Sigve On 28 May 2014, at 01:01, Michael Lawrence wrote: > I think you want to use VRanges. See ?VRanges. You can use readVcfAsVRanges to get one from ...
cancer written 5.5 years ago by Sigve Nakken • 50 • updated 5.5 years ago by Michael Lawrence ♦ 11k
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Comment: C: VCF class: different length when unlisting INFO CompressedCharacterList
... On 28 May 2014, at 14:26, Michael Lawrence wrote: > > > > On Wed, May 28, 2014 at 2:42 AM, Sigve Nakken wrote: > Hi, > > readVcfasVRanges works! Makes life much easier for me. Thanks so much for the clarification:) It cannot seem to find the “FILTER” column in the resulting ...
written 5.5 years ago by Sigve Nakken • 50
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Comment: C: VCF class: different length when unlisting INFO CompressedCharacterList
... Hi, readVcfasVRanges works! Makes life much easier for me. Thanks so much for the clarification:) It cannot seem to find the “FILTER” column in the resulting DataFrame however, yet i specified this in my ScanVcfParam object, e.g.: info_tags <- rownames(info(scanVcfHeader(filtered_vcf))) vcfpara ...
written 5.5 years ago by Sigve Nakken • 50
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VCF class: different length when unlisting INFO CompressedCharacterList
... Hi, I’ve had similar challenges as Francesco, and have unsuccessfully tried to use the data structures and functions provided by VariantAnnotation. My experience is that I need the ‘expand' functionality more often with respect to the samples rather than the annotation tags. And as my experience wi ...
cancer written 5.6 years ago by Sigve Nakken • 50 • updated 5.5 years ago by Michael Lawrence ♦ 11k

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Popular Question 3.5 years ago, created a question with more than 1,000 views. For readVcfAsVRanges + FilterRules
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