Questions tagged [gwas]
A genome-wide association study (GWA study), also known as whole genome association study (WGA study or WGAS), is an examination of many common genetic variants in different individuals to see whether any variant is associated with a trait. [Wikipedia]
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questions with no upvoted or accepted answers
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Including covariates makes QQ plot worse
I know this is similar to this question, but that one didn't seem to get a satisfactory answer.
I'm using plink to run a GWAS. My phenotype data are binary, so it's performing a logistic regression ...
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3
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Fisher's method for P-value more conservative than OLS?
I am currently observing an interesting phenomenon in my analysis. I have a simple logistic regression model for independent Inds. The model is as follows:
$$\operatorname{logit}(Y) = \beta_0+\...
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2
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How to estimate the phenotypic variation explained by top SNPs from a GWAS study?
I have conducted a large-scale GWAS study and got a few significantly associated SNPs. I used GEMMA with -lmm 1 options to run ...
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multivariate cox regression - combining genotypes for each SNP
For 53 SNP I have coded genotypes as 0 for aa, 1 for ab, and 2 for bb for 29 samples and I have outcome and time to outcome. Here outcome is called "BCR" below.
I am using the survival package in R ...
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How to analyse GWAS data of co-morbid disorders?
Lets say I am running a GWAS for a disease condition O , where all my cases has one or more of the following diseases: A, B, and C, in addition to my outcome of interest O. So I include individuals ...
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2
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Meta-analys of GWAS and interpretation of estimated p-values
I'm a bit confused about a meta-analysis performed with PLINK on two studies.
The statistics look like this for a specific SNP in each study:
Study_1: OR = 3.657, SE = 0.336, p= 0.0001137
Study_2: ...
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1
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0
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Is there a way to adjust FDR threshold using correlation across tests (aka, number of estimated independent tests, like in Bonferroni correction)
For Bonferroni correction, correlations can be used to inform correction of multiple testing using the spectral decomposition of matrices. For example, in GWAS, the threshold is established to be 5e-8 ...
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How to construct a linear mixed model for GWAS with SSR markers?
I would like to construct a linear mixed model using SSR markers. I have the phenotype vector, SSR marker matrix, and the covariance matrix for the random effect (used to control the population ...
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1
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0
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220
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Why don't my GWAS QQPlots look the same?
I am trying to create a QQPlot of 100 log-transformed p values from a GWAS study. The idea is that taking the -log(p) will magnify the smallest p values to make them easier to see. (reference)
I was ...
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1
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84
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R or spss? For a conditional regression with 2 dependent variables?
Maybe you find my question a bit simple but I'm really confused as I'm not statistician.
I have 2 SNPs (can be proposed 2 genes instead) that are related to a primary disease (like major depression), ...
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1
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50
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Replication after Meta-Analysis in a multiple testing situation?
I was recently in an introductory seminar about Genome Wide Association Studies (GWAS). These studies aim to examine if any genetic markers are associate with a certain trait. It is not uncommon to ...
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1
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0
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79
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Adjusting for population substructure in heterozygosity values using regression with principal components
I'm working on some sample level QC for a large genome wide association study and while reading through the QC documentation for the UK Biobank project, I came across this part, discussing a technique ...
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1
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0
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129
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Elastic net is being used in genome wide analysis. Similar approach would work for survey analysis?
I'm approaching the elastic net procedure for genome wide analysis (GWAS) because it allows for feature selection, groups detection and improved validity.
It's a powerful technique when you have many ...
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125
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How to correct deflated p value distribution from qqplot in PWAS/GWAS
I'm conducting regression analysis using R of the ability of several hundred proteins (and other covariates) to predict ventricle volume in a human sample. As is common in GWAS/PWAS research, I ...
0
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Test to find expected outcome
I have a list of genes and I tested if these genes are associated with a disease by using the genome-wide association summary statistics dataset. Chi-square statistics was used and after performing ...
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1
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91
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Estimating heritability from twin studies--How to get it?
I was learning the concept of heritability, and come to the Falconer's formula:
$h^2=2(r_{MZ}-r_{DZ})$ (1)
Where $r_{MZ}$ and $r_{DZ}$ are correlation coefficients of ...
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Calculate Beta and se from GWAS summary
I have some metaGWAS data which has only odds ratio and P values. Can I estimate standard error and effect size from these data?
(EX)
rsID Allele1 Allele2 odds P
rs12878 A T ...
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How should I interpret a weighted genetic risk score?
I created a weighted Genetic Risk Score (GRS) by summing the product of the SNP-dosages times their regression coefficients from the GWAS in which I found them. So:
...
