User: sviatoslav.kendall

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Posts by sviatoslav.kendall

<prev • 43 results • page 1 of 5 • next >
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Filter out Non-Diploid segments in FACETS data
... I've got some sequencing data (tumor/normal pairs) that has had mutations called and also been subjected to copy number analysis using [FACETS][1]; these two analyses have been merged such that each mutation has been mapped to a FACETS segment and the associated values. I want to run an analysis t ...
R facets cnv sequencing written 12 weeks ago by sviatoslav.kendall420
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Question about Copy-Number Data produced using Sequenza
... I have a list of mutations and want to filter out mutations that are non-diploid or have been amplified or deleted. The data I'm working with had mutations called using [MuTect][1] and copy-number data produced using [Sequenza][2]. I do not have access to the raw sequencing data so I can't re-ru ...
R sequenza copy-number written 3 months ago by sviatoslav.kendall420 • updated 6 weeks ago by Biostar ♦♦ 20
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Answer: A: DNA differential methylation analysis for Illumina Human Methylation 450k and 27
... I think you should be OK doing that but pay attention to which reference genome you're using. I think the 27K probes might be based on an older build than the 450K. ...
written 4 months ago by sviatoslav.kendall420
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Answer: A: survival analysis with a continuos variable
... When I do survival analysis with a continuous variable as the predictor, I use the coxph() function something like this: coxph_obj = coxph(Surv(my_Data$Survival_Time, my_Data$Survival_Event) ~ my_Data$Continous_Variable) But here's an older post that you might find helpful: https://www.biostar ...
written 5 months ago by sviatoslav.kendall420
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Comment: C: Colors in IGV
... The link to IGVs default-color documentation did not work for me but it looks like it was point to [this page][1] [1]: http://software.broadinstitute.org/software/igv/AlignmentData ...
written 8 months ago by sviatoslav.kendall420
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SNPEFF Sequence Ontology Terms that are equivalent to a Loss of Function
... I'm writing a script that will identify loss of function mutations in a [SNPEFF][1]-annotated MAF file containing point mutations, indels or, in some cases, both. So far, I've been doing this is by typing up a list of every [Sequence Ontology][2] value that indicates a loss of function: stop_gaine ...
snp sequencing written 11 months ago by sviatoslav.kendall420 • updated 9 months ago by Biostar ♦♦ 20
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Comment: C: Majors for a career in Bioinformatics
... Since you definitely like biology, I suggest you start there by taking bio and bio-relevant classes (chemistry, physics, math, etc). Your declared undergraduate major is far less important to your career than the background knowledge and skills you develop during it - especially for interdisciplinar ...
written 11 months ago by sviatoslav.kendall420
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Comment: C: Diff exp analysis of 450k methylation data, what is appropriate, logistic or li
... Yes, a three-level logistic regression on a subset of highly-variable probes seems sensible although I've never done it as formally as all that. My approach has generally been to: 1. Sort loci by decreasing between-samples variance 2. Select the most-variant 5, 10, 25% of loci 3. Plot a heatmap w ...
written 11 months ago by sviatoslav.kendall420
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Answer: A: Diff exp analysis of 450k methylation data, what is appropriate, logistic or li
... I would start by restricting my focus to a subset of loci whose beta values show the highest degree of between-samples variance and make some heatmaps with your variables as annotations. Changing up what how many loci you filter out and what sort of clustering method/distance you use will help you s ...
written 11 months ago by sviatoslav.kendall420
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In FACETS, what does the mafR value represent?
... I've been working with some copy number data produced using [FACETS][1] and I'm just wondering if anyone knows what the "mafR" values represent. I've read the documentation but found nothing explaining what this value means. [1]: https://sites.google.com/site/mskfacets/ ...
cnv written 11 months ago by sviatoslav.kendall420 • updated 10 days ago by bruce.moran240

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