All Questions
Tagged with gwas statistics
10
questions
2
votes
2
answers
413
views
How to z-transform Fst and -log(p) values for genome wide selection scan?
I saw in the literature a lot genome wide scans showing $F_{ST}$ values in a 'z-transformed' format which seems to be bounded between 0 to infinity.
Examples are found easily searching for 'genome-...
- 121
2
votes
1
answer
315
views
Genomic inflation factor distribution (lambda)
Considering that the p-value of a chi statistic(df=1) is uniform, the expected genomic inflation factor is λ=1. I show its calculation in R with the next chunk of code:
...
- 73
1
vote
2
answers
133
views
Why is the p-value significance threshold for HLA association tests $5*10^{-8}$? [closed]
Typically, a p-value of $p<=5*10^{-8}$ is used for genome-wide association testing, as there are roughly $1/p$ independent LD blocks in the human genome, so it correct for multiple testing across ...
- 1,719
4
votes
1
answer
158
views
LD Score Regression Derivation hard to follow
I am trying to understand the derivations from Sullivan et al. (2015) in the Supplementary Material. There, it is mentioned in the first page that the least squares estimate of the j-th SNP effect, ...
0
votes
2
answers
88
views
Question about the practical relevance of chromosome position and p-value
Article of interest: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3023908/#SD1
Referring to Figure 2b of that article, if I understand correctly, the x-axis refers to the position of each variant in a ...
0
votes
1
answer
155
views
Odds ratio and enrichment of SNPs in gene regions?
I did a QTL analysis with a panel of 7M SNPs, and want to analyze the enrichment of the significant qtl-SNPs in different genic regions (promoters, gene bodies, TFBS, etc.).
A straightforward way to ...
- 35
0
votes
2
answers
122
views
Should you filter GWAS hits with high standard error?
I'm trying to figure out if I should be filtering out GWAS hits that have high standard error and I'm not quite sure what to do. It seems like it might not matter, because the standard error is used ...
- 831
3
votes
1
answer
112
views
What is the state of the art for GWAS in terms of the statistical algorithm for either Case/control and Quantitative traits?
This question was also asked on Biostars
I'm trying to understand what is the best algorithm for GWAS nowadays.
I know we have many tools available like Plink and Hail, but currently, what is the ...
- 207
3
votes
3
answers
1k
views
Is there a way to do GWAS on phenotype data that is not normally distributed?
Is there a way to do GWAS on phenotype data that is not normally distributed?
For example, if you were measuring a trait as a proportion, and the majority of the data consisted of 0.00 with a long ...
- 69
5
votes
1
answer
1k
views
Adjusting phenotypes by regressing out covariates
I'm trying to use the bfGWAS tool, which analyses GWAS data and integrates functional annotations to identify casual SNPs (paper and
github). In the user manual, it states:
We recommend first ...
- 153