User: doodle

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doodle30
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Posts by doodle

<prev • 21 results • page 1 of 3 • next >
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Permutation of Fst statistics of genotyped data to get p value
... Hello, I have genotyped data of two populations in plink format. I need to do permutation to calculate Fst to obtain empirical p values. Plink doesn't have the provision to do it for Fst. Can you please help me with a software and method to do so? I've been trying to do this for over a month and ge ...
pvalue fst plink empirical pvalue genotype written 3 months ago by doodle30
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Permutation of Fst statistics of genotyped data to get p value
... Hello, I have genotyped data of two populations in plink format. I need to do permutation to calculate Fst to obtain empirical p values. Plink doesn't have the provision to do it for Fst. Can you please help me with a software and method to do so? I've been trying to do this for over a month and ge ...
pvalue fst plink empirical pvalue genotype written 3 months ago by doodle30
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Comment: C: Post Fst calculation analysis
... I'm unable to show the data as a table here... ...
written 4 months ago by doodle30
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Post Fst calculation analysis
... Hello, I have calculated genome-wide Fst of SNP loci in 2 populations in Plink which uses VCF-tools's Fst estimator and got the following output : CHR SNP POS NMISS FST 1 1:58460 58460 5732 -8.33795E-05 1 1:64904 64904 5732 -8.33795E-05 1 1:70728 70728 5731 0.000447608 1 1:77646 77646 573 ...
population structure diversity loci fst snp written 4 months ago by doodle30
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How to begin with Fst calculation of SNPs from two different populations
... Hello, I have two different populations and have identified a set of variants whose frequencies differ in the two populations. I now need to calculate Fst for those SNPs to identify genomic selection. I'm not able to figure how to start with the work. I have imputed data for the SNPs in gen.gz form ...
populations fst snp written 4 months ago by doodle30
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Comment: C: Post PCA analysis
... Hi Kevin, I'm still a little stuck with this work. Can I please know what you meant when you wrote 'People do use principal components as 'phenotypes', sometimes. So, you can use it if you wish. PCs are uncorrelated, which can help in the context of a regression model' in the comments above? Just ...
written 8 months ago by doodle30
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Comment: C: Post PCA analysis
... Yes, the results are different. Okay, will try out your step 3. Thanks! ...
written 8 months ago by doodle30
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Comment: C: Post PCA analysis
... The overall aim is to identify age at diagnosis of diabetes in 2 populations. 1.I did a GWAS for age at diagnosis for the first population. 2.Next, I merged the data of the 2 populations and did a PCA on them. I got 2 different clusters. 3.Next, I was asked to run a GWAS using the first PC as a p ...
written 8 months ago by doodle30
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Comment: C: Post PCA analysis
... So I did a GWAS using the first principal component as a phenotype and plotted a manhattan plot. I got a few hundred hits (above the 5* e -8) Is that normal? My next step would be to use the top hits as covariates for the GWAS on my main phenotype. ...
written 8 months ago by doodle30
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Comment: C: Post PCA analysis
... Beautiful! Thank you so much Kevin! It has been of immense help. ...
written 8 months ago by doodle30

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