User: rednalf

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rednalf20
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Posts by rednalf

<prev • 25 results • page 1 of 3 • next >
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Estimate heritability of a trait (single number)
... I am interested in calculating the heritability of the trait for which I performed a GWAS. I have been using gcta (`gcta64 --bfile test --make-grm --out test`), but how can I now get down to a single value that summarizes the heritability (e.g. 5%)? ...
genome snp written 11 days ago by rednalf20
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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 5 months ago by rednalf20
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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 7 months ago by rednalf20
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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 7 months ago by rednalf20
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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 7 months ago by rednalf20
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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 9 months ago by rednalf20 • updated 9 months ago by Kevin Blighe37k
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Comment: C: Inverse normal transformation
... Yes a lot, thank you very much for your (fast) help! ...
written 9 months ago by rednalf20
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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 9 months ago by rednalf20
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Comment: C: Inverse normal transformation
... Thank you. I have considered log, square root, cube root and Johnson transformation for now. I will have a look at DESeq2. What do you think about the inverse normal transformation and the script based on Yang et al.'s paper? ...
written 9 months ago by rednalf20
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Comment: C: Inverse normal transformation
... Thank you for your comment - the information has been added to the initial post. ...
written 9 months ago by rednalf20

Latest awards to rednalf

Great Question 5 months ago, created a question with more than 5,000 views. For PLINK 1.9 - Converting PED/MAP to BED/BIM/FAM with missing values
Popular Question 9 months ago, created a question with more than 1,000 views. For PLINK 1.9 - Converting PED/MAP to BED/BIM/FAM with missing values
Popular Question 2.1 years ago, created a question with more than 1,000 views. For PLINK 1.9 - Converting PED/MAP to BED/BIM/FAM with missing values

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