User: lillo.sim

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lillo.sim40
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United Kingdom
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4 years, 3 months ago
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Posts by lillo.sim

<prev • 19 results • page 1 of 2 • next >
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Comment: C: Convert between formats for names of indels
... Thanks Emily, this seems very clever. Do you know if there is a way using biomaRt to request the upstream position based on rsids in one go, or do you think I first need to find the chr:pos for each of the variants listed in the rsids object, and then in a second step find the alleles at their chr:p ...
written 4.5 years ago by lillo.sim40
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Comment: C: Convert between formats for names of indels
... Thank you for your reply! But even if I go one base before I am still having trouble with finding the "other" allele using biomaRt, so for example how would I know to convert  rs146107628 -/T 10 100002842 --> 10:100002841:C_CT I R If I don't know that the other allele is C, ...
written 4.5 years ago by lillo.sim40
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Convert between formats for names of indels
... Hi, I have a list of INDELS in their rsid format, and I am trying to convert this list from the rsids to a format like the one coming out of the imputation from MACH/Minimac, i.e. chr:pos:ALLELES. I have tried using biomaRt to find the chr, positions, and alleles corresponding to the rsids like th ...
R biomart indels written 4.5 years ago by lillo.sim40 • updated 4.5 years ago by Emily_Ensembl17k
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Comment: C: Allele frequencies for ALL of the variants in 1000Genomes: direct download?
... Thank you Giovanni! This is still a limited set of SNPs (N= 10,836,459), so I will still keep trying to find another way, but in the meantime this helps! ...
written 4.8 years ago by lillo.sim40
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Comment: C: Allele frequencies for ALL of the variants in 1000Genomes: direct download?
... Thank you for your reply and suggestion Charles, I have written to the 1000 Genomes to ask for a direct link for the frequencies for all of the variants, I will post their answer here as soon as I get one if it helps someone else.  ...
written 4.8 years ago by lillo.sim40
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Allele frequencies for ALL of the variants in 1000Genomes: direct download?
... Hi, I am trying to find the minor allele frequency of all of the SNPs and INDELs from the 1000Genomes EUR reference. It was taking too long to compute the frequencies of ALL the variants using vcftools as outlined here https://www.biostars.org/p/6897/, so I tried extracting the allele frequency re ...
snp sequencing written 4.8 years ago by lillo.sim40 • updated 16 months ago by Biostar ♦♦ 20
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Software for power analysis in meta-analysis: compute the maximum significance needed by an additional sample for meta-analysis to reach genome-wide significance
... I have an association study analysis (GWAS) that does not reach genome-wide significance (max p-value <10E-5), and there is a potential additional sample (so with known N and known effect size/SE for each association) that we want to use together with the GWAS to conduct a fixed effect meta-analy ...
R written 4.8 years ago by lillo.sim40
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Locuszoom Standalone Change X-Axis And Use The Plots In A Script
... I am using the standalone LocusZoom software,but I am having two problems: I have to create a plot showing only position on the x-axis (not showing the genes). If I just use showGenes=FALSE with nothing else the genes still appear, but if I use rfrows=0 then the genes are not shown, but the problem ...
R written 5.4 years ago by lillo.sim40
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Comment: C: How To Annotate Many Ensembl Gene Ids To Find The Function Of Each Gene And Invo
... This seems like a nice package, I'll try it out now! thank you ...
written 5.6 years ago by lillo.sim40
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Comment: C: How To Annotate Many Ensembl Gene Ids To Find The Function Of Each Gene And Invo
... Thank you Alex, but biomaRt doesn't seem to contain enough clinical information, unless I am using it incorrectly? library(biomaRt) mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl") results <- getBM(attributes = c("clinical_significance"), filters = "ensembl_gene_id", v ...
written 5.6 years ago by lillo.sim40

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