User: Sam
Sam • 2.2k
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Posts by Sam
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... You can use the z-score for PRS calculation as long as your target and base are from the same population. ...
written 2 days ago by
Sam • 2.2k
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... You can try using [GCTA GREML-KIN][1] which can take into account of relateship information when calculating the SNP heritability
[1]: https://cnsgenomics.com/software/gcta/#Overview ...
written 2 days ago by
Sam • 2.2k
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... If I remember correctly, that blog was written with Polygenic Score Analysis in mind where Clumping is preferred. The reason why clumping is preferred in Polygenic Score analysis is that we want to maintain the SNPs that has the strongest signal (lowest p-value). With pruning, the SNPs were randomly ...
written 3 months ago by
Sam • 2.2k
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... Maybe just check the number of reads that show this kind of problem. If the number is small, just remove them ...
written 3 months ago by
Sam • 2.2k
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... Unfortunately, that's like 3 years ago and I have no memory of that. I think @Ian's answer should most likely be what's happening ...
written 3 months ago by
Sam • 2.2k
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Answer:
A: Base file of PRSice software
... The base file is a GWAS association file. Usually you can obtain it from external data base (e.g. PGC). For Type 2 Diabetes, you might be able to get the summary statistics from WTCCC. Alternatively, if you have an independent data set (independent to your target data), you can also perform the GWAS ...
written 4 months ago by
Sam • 2.2k
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... The thing is, we only perform clumping on SNPs that were found in both the target and base file. By using the imputed data, you increase the coverage and might result in more post-clumped SNPs, therefore increase amount of information and possibly increase the performance of your PRS model ...
written 4 months ago by
Sam • 2.2k
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... I'd suggest you to perform a partitioning of heritability and see if majority of the heritability lies within these regulatory elements. [LDSC][1] is one of the tool that can perform that
Though the problem of this approach is that it doesn't provide you with a SNP based probability
[1]: https:/ ...
written 16 months ago by
Sam • 2.2k
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Comment:
C: 1000 genomes PCA for whole genome
... You can read [here][1]. Though I do suggest you to follow Kevin's tutorial
[1]: https://www.cog-genomics.org/plink/1.9/input#vcf_filter ...
written 16 months ago by
Sam • 2.2k
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Comment:
C: 1000 genomes PCA for whole genome
... As mentioned by GabrielMontenegro, you will need to do the following:
1. clean the multi-allelic sites from your files
2. remove or rename duplicated SNPs
3. perform pruning using either `--indep` or `--indep-pairwise`
4. Extract pruned SNPs with `--extract`
5. perform PCA using `--pca`
(You can ...
written 16 months ago by
Sam • 2.2k
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