All Questions
18
questions
1
vote
2
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70
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Why does my HWE QQ plot have extreme deviation and what does it mean?
This question was also asked on Reddit
I have recently completed my thesis and one of the comments was that I report on why this graph looks this way. I have tried to find a reason but the closest I ...
2
votes
1
answer
522
views
Getting nearest gene from SNP data using SNP ID, CHR, and BP
I have data from a GWAS that provides me with the SNP, Chromosome, and base-pair. My data set has thousands of SNPs. What is the easiest way to find the nearest gene for each SNP using this ...
- 21
0
votes
1
answer
91
views
Regression plot of a continuous trait - is there a binary equivalent?
Within the GWAS wikipedia page, you can view the following plot:
"Illustration of a simulated genotype by phenotype regression for a
single SNP. Each dot represents an individual. A GWAS of a ...
- 155
0
votes
2
answers
191
views
HG19 Position meaning
I am looking at genomic data (HG19). I have many SNPs, their chromosomes and positions.
I want to look at certain SNP (suppose its chromosome is 1 and position 77,226,919), and extract all SNPs in ...
- 251
3
votes
1
answer
647
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 ...
- 75
1
vote
1
answer
79
views
Random GWAS data generator
I was wondering if there is a tool/script/program that randomly generates GWAS data. The purpose of such a tool would be to use it for educational purposes. So you generate some random .ped, .map and ...
2
votes
2
answers
74
views
Loss of predictive power of polygenic risk score when dataset contains missing variants
I am trying to calculate polygenic risk scores (PRS) scores for a new dataset. This dataset does not have all the variants that the PRS score needs. The PRS score I am interested in has 40 variants, ...
- 21
1
vote
1
answer
70
views
Apply trained PRS on another dataset
I am using PRSice to compute the PRS over a train set and want to use the coefficient used on the train set to apply it on another set which I will call the test set.
Once I compute the PRS I get a ...
- 113
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
1
vote
1
answer
2k
views
Convert VCF to genotype table
How can I convert a VCF file into a genotype table (SNP matrix)?
I have this format:
...
- 147
0
votes
1
answer
122
views
How to analyze co-occurrence of multiple SNPs?
I am interested in 20 different SNPs that all are either As or Gs, and they all occur on the same chromosome. How can I assess the co-occurrence of these SNPs? In other words, I want to know, if SNP1 ...
- 151
1
vote
2
answers
255
views
Simulating phenotype with the 1000 Genomes Project
I'm looking for a way to simulate phenotypes against a real SNP data source, such as the 1000 Genomes. It must be free for commercial purpose (Eg.: MIT license). Any recommendation?
I'm trying to use ...
- 207
0
votes
1
answer
65
views
significant SNPs to annotated candidate genes
I have performed GWAS and got some significant SNPs. How can I get candidates genes in the flanking regions of those SNPs and also their functional annotations (eg. KEGG).
5
votes
2
answers
3k
views
What does PCA mean on GWAS
I understand what GWAS is and I'm able to perform certain tests with the p-values, etc. But what I am having a hard time wrapping my head around is what PCA on GWAS means.
So let's say I have 100,000 ...
- 341
3
votes
1
answer
88
views
Assuming that we have the following SNP and phenotype data, is the SNP significantly associated with the phenotype?
So if I attempt this question using their method I put the data of genotype and phenotype into a data frame in R then use lm() to do linear regression and ...
- 33