User: rednalf

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rednalf60
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Posts by rednalf

<prev • 27 results • page 1 of 3 • next >
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Mendelian randomisation and covariates
... I am using mendelian randomisation (MR) approach to determine whether there is a causal effect of an exposure *X* on the outcome *Y*. To do so, I run a genome-wide association study (GWAS) of the outcome *Y*, adjusted for multiple covariates, among which the exposure term *X*. Do I lose every signal ...
genome gwas mr mendelianrandomisation snp written 3 months ago by rednalf60
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How to convert PLINK data files to bgen and bgen.bgi files?
... For a specific script, I need genotyping data in .bgen and .bgen.bgi format. How can I obtain those formats starting from PLINK data files? ...
genome snp written 5 months ago by rednalf60 • updated 5 months ago by chrchang5236.7k
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Estimating heritability of a trait from data containing siblings
... Does it make sense to estimate the heritability of a trait from data containing siblings? Due to the presence of siblings, the estimate will be much higher in the sample, right? ...
genome snp written 6 months ago by rednalf60 • updated 6 months ago by Lemire560
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Post-imputation graph: Posterior probability vs. Empirical CDF
... This plot is showing the distribution of the posterior probabilities of the most likely alleles for KIR2DS4TOTAL locus, shown as an empirical cumulative distribution function. What does this mean biologically? My knowledge in statistics is unfortunately quite poor... Note: two curves are plotte ...
genome written 19 months ago by rednalf60
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Comment: A: Obtain genotype data from Eurasian and HapMap populations
... Sure, it is Supplementary Figure 21 of https://www.nature.com/articles/s41590-018-0049-7 ...
written 21 months ago by rednalf60
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Comment: C: Obtain genotype data from Eurasian and HapMap populations
... Thank you Kevin for your answer. I have been doing PCAs using 1KG data (CEU, GIH, MEX, TSI, YRI, etc.) and your tutorial (thank you btw), but since my cohort is French I was interested in plotting my samples with cohorts with a more precise ancestry (only Eurasians) to see if they overlap with Frenc ...
written 21 months ago by rednalf60
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Obtain genotype data from Eurasian and HapMap populations
... I have seen this figure in a Nature Immunology paper. I was wondering where I can find the genotype data from the 36 populations (32 Eurasian populations and 4 HapMap populations) in panel b. Do you know if it is open access? I couldn't find anything online. ![Nature Immunology Figure][1] [1] ...
genome snp written 21 months ago by rednalf60
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Yeo-Johnson and Logarithmic transformation
... Is a Yeo-Johnson transformation using a lambda equal to 0 the same transformation as a logarithmic transformation? ...
R transformation yeo-johnson logarithm statistics written 23 months ago by rednalf60 • updated 23 months ago by Kevin Blighe56k
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Comment: C: Inverse normal transformation
... Yes a lot, thank you very much for your (fast) help! ...
written 23 months ago by rednalf60
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Comment: C: Inverse normal transformation
... I found it in the Supplementary Information, page 18 (https://media.nature.com/original/nature-assets/nature/journal/v490/n7419/extref/nature11401-s1.pdf) ...
written 23 months ago by rednalf60

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