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Results tagged with gwas
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user 3848
2
votes
What does PCA mean on GWAS
Point 1
PCA on all GWAS is attempting to assess that the genetic variation between diseased and healthy people is evening spread across the genome. …
M__♦
- 13k
2
votes
Accepted
Pandas automatically rounds GWAS P-value
The solution you likely want is here,
pd.set_eng_float_format(accuracy=x, use_eng_prefix=True)
x = whatever is required
The function set_eng_float_format has been moved around a bit and is now a to …
M__♦
- 13k
1
vote
Power calculation for GWAS/EWAS
Interesting question I would recommend the effective population size $N_{e}$, and error bars around this. Ne can be calculated via $F_{st}$ and is perhaps the most important parameter to determine th …
M__♦
- 13k
1
vote
Accepted
Excess average estimated identical-by-descent in genotype data
A clear negative association within an inbreeding coefficient suggests convergent evolution driven by shared selective pressure. There is an outside chance of purifying selection, or else balancing se …
M__♦
- 13k
1
vote
Accepted
Random GWAS data generator
Agreed with the above I would use an existing dataset from NCBIs dbSNP here
Random doesn't work well because HW signal will be meaningless as soon as the Jukes-Cantor distance is exceeded (which it wi …
M__♦
- 13k
1
vote
Why is the p-value significance threshold for HLA association tests $5*10^{-8}$?
Its a very good question and it is also a good study. What you are saying must be correct.
I thought it was possible they used the correct critical probability in the original submission and a reviewe …
M__♦
- 13k
1
vote
How to z-transform Fst and -log(p) values for genome wide selection scan?
@JRodrigoF is the correct answer. I'll attempt to explain why the z-score is being used, because it is not immediately obvious.
$F_{ST}$ is not trivial for anyone to understand per se. It is extremely …
M__♦
- 13k
0
votes
Accepted
Interpreting GWAS results with different settings
The genomes under analysis are under predominant linkage disequilibrium, i.e. linkage. Chromosome 1 shows strong (or stronger - cut-off depending) HW signal as do one or two telomeres - telomeres are …
M__♦
- 13k
0
votes
Accepted
Apply trained PRS on another dataset
The coefficient is the third column from the right, you can tell because some are positive and other negative. When the value is negative the association is a negative correlation. When it is positive …
M__♦
- 13k
0
votes
Loss of predictive power of polygenic risk score when dataset contains missing variants
Which software package around you using, PRSice? Generally missing values comprising half the total observations are extremely difficult to calculate using regression analysis (or many statistical ana …
M__♦
- 13k
0
votes
Is there a way to do GWAS on phenotype data that is not normally distributed?
Sure, you would use the negative binomial distribution when the majority of data was around 0. In other words the data is clustered with the standard deviation far greater than the mean. Most general …
M__♦
- 13k
0
votes
Why does my HWE QQ plot have extreme deviation and what does it mean?
factors) resulted in a stronger fit by for example 3 logs difference, whilst the genetic model is 50 logs difference, then that is the answer and points to the need for careful population sampling for GWAS …
M__♦
- 13k