Skip to main content

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]

Filter by
Sorted by
Tagged with
8 votes
1 answer
301 views

Fisher's exact test vs. differential gene expression

I identified SNPs that are associated with phenotype through GWAS. I labeled the types of genetic variants in those significantly associated SNPs and now I'm trying to assess the association of those ...
mango's user avatar
  • 103
2 votes
1 answer
111 views

Interpreting Fisher's exact test OR, CI and p-values

In the context of Fisher's exact test results, it seems that a bunch of online tutorials mainly focus on interpreting the p-value exclusively, without considering the confidence intervals or the odds ...
mango's user avatar
  • 103
1 vote
0 answers
39 views

Why my GWAS p-value QQ-plot falls far above diagonal? [duplicate]

I'm trying to run GWAS pipeline using plink, but the results I got look really off. The QQ-plot of the p-values is far above the diagonal. I'm pretty sure I followed the correct QC process, and the ...
Celia L.'s user avatar
2 votes
1 answer
118 views

P-values too low to plot [closed]

In my GWAS analysis, I got some very low p-values (I have a very large dataset), below E-600. R Studio is not able to plot the values below E-300. Do you have any suggestions on how to plot these, and ...
A29's user avatar
  • 21
0 votes
0 answers
146 views

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 ...
Samuel Bateman's user avatar
1 vote
0 answers
15 views

how to know the p value of the association between a phenotype and a variant (fixed effect) when using linear mixed effect model [duplicate]

I am doing gwas analyses using twins data. after quality control in plink, over 6 millions variants and 2400 individuals are left for conducting association analyses. i didvided the variants into 22 ...
Zhoufeng Ye's user avatar
0 votes
1 answer
103 views

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 ...
Raymond's user avatar
  • 11
1 vote
1 answer
4k views

What is the inverse normal transformation (INT) and what are the reasons behind using it?

I noticed a statistical method called inverse normal transformation in the following research article FTO genotype is associated with phenotypic variability of body mass index. I attached the ...
7-x's user avatar
  • 11
1 vote
0 answers
48 views

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 ...
Albert Ying's user avatar
1 vote
1 answer
382 views

Use of Bayesian Regression and the Multiple Testing problem

In many association studies (e.g., GWAS), a large number of Linear Regression models are fitted. Then, a strategy to account for the Multiple Testing issue is adopted (e.g., Bonferroni). That being ...
wrong_path's user avatar
2 votes
0 answers
284 views

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 ...
Anik Dutta's user avatar
1 vote
0 answers
97 views

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 ...
purod's user avatar
  • 305
0 votes
0 answers
463 views

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 ...
Jiang's user avatar
  • 1
0 votes
0 answers
57 views

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: ...
George Talford's user avatar
1 vote
0 answers
223 views

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 ...
Hank Lin's user avatar
  • 529
12 votes
1 answer
311 views

How do children manage to pull their parents together in a PCA projection of a GWAS data set?

Take 20 random points in a 10,000-dimensional space with each coordinate iid from $\mathcal N(0,1)$. Split them into 10 pairs ("couples") and add the average of each pair ("a child") to the dataset. ...
amoeba's user avatar
  • 105k
3 votes
1 answer
2k views

Principal components as covariates in a linear model

I'm working with some genetics data, performing linear regressions, and have been advised to control for population structure by performing principal components analysis. My model at the moment is of ...
Erika_Hammerl246's user avatar
2 votes
0 answers
248 views

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 ...
user3324491's user avatar
2 votes
0 answers
51 views

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 ...
Veera's user avatar
  • 549
0 votes
1 answer
200 views

Small values are sorted incorrectly, subset() gives wrong data in R [closed]

I have a (gwas-)data where one column is p-value. P-values vary from $1*10^{-8}$ to $1$. I would want to have a subset where I have only values where p-value is $5*10^{-5}$ or lower. I have the ...
Jaakko L's user avatar
1 vote
0 answers
84 views

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), ...
Sarah's user avatar
  • 11
1 vote
2 answers
397 views

software for genome wide associations studies (GWAS) [closed]

I have just started learning about genome wide associations studies (GWAS) as I will have to run some of them in the near future, and I am pretty confused about which are the best computational tools ...
fastDio's user avatar
  • 11
1 vote
0 answers
51 views

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 ...
DUWUDA's user avatar
  • 231
1 vote
0 answers
79 views

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 ...
Vivek's user avatar
  • 111
1 vote
1 answer
358 views

Ordered Logistic Regression GWAS

I am attempting to do an ordered logistic regression in R on SNP matrixes (presence absence matrix 1 or 0) with three outcomes (1,2,3). I am having an issue of 0 p-values when low numbers (<5%) ...
SemiQuant's user avatar
5 votes
1 answer
4k views

Deflated QQ plots in genome-wide association studies

I am working on a GWAS dataset containing 920 individuals with genotype information on ~1.5M SNPs (genotyped on Illumina 2.5omni chip; no imputed SNPs). I am testing several different phenotypes in ...
motu's user avatar
  • 51
4 votes
1 answer
2k views

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 ...
njc's user avatar
  • 75
2 votes
0 answers
103 views

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: ...
eXpander's user avatar
  • 574
3 votes
0 answers
123 views

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+\...
Adam's user avatar
  • 31
1 vote
2 answers
8k views

Interpretation of P values in Genome Wide Association Studies

Genome wide associate studies (GWAS) are a common method used in associating single nucleotide polymorphisms (SNPs) to a disease or trait under study. I don't work in this field and I'm always ...
user2157668's user avatar
1 vote
0 answers
129 views

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 ...
Bakaburg's user avatar
  • 2,927
9 votes
1 answer
6k views

Case-control study and Logistic regression

Suppose we have case-control data, where cases have some disease ($Y$) and controls don't and we are interested in the association of some other variable(s) ($X$). I know that in this scenario we ...
bdeonovic's user avatar
  • 10.1k
4 votes
1 answer
3k views

Inflated p-value after adjusting for covariates, in GWAS

I am working on some GWAS (Genome-Wide Association Studies) now. A genome scan was done for all the SNPs, with first 3 principal components adjusted (PCs are used for adjusting ethnicity effect) and ...
VincentShen's user avatar
1 vote
0 answers
205 views

Expected effect of each single-nucleotide polymorphism (SNP) in a genome-wide association study (GWAS) [closed]

It was mentioned in a genetics class that in a genetic association analyses of a trait with all SNPs, it is possible to compute the expected effect of each SNP with the trait using the correlation ...
Richard's user avatar
  • 19
25 votes
1 answer
22k views

In genome-wide association studies, what are principal components?

In genome-wide association studies (GWAS): What are the principal components? Why are they used? How are they calculated? Can a genome-wide association study be done without using PCA?
suprvisr's user avatar
  • 693