User: Sam
Sam • 2.6k
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Posts by Sam
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... I have a rough Nextflow pipeline for this. You can find the scripts [here][1]
You can read the help message to see what file you need and you can read the script to see what actually did the script does.
You will also need the GreedyRelated program I wrote to run the script, which can be found [h ...
written 1 day ago by
Sam • 2.6k
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... It'd be much easier to use PLINK than to use R for this type of analysis.
The error message suggested some of the SNPs has duplicated name (e.g. ".", which is typical when you convert vcf to PLINK format). You will need to do some preprocessing beforehand. Might want to look into the PLINK manual ...
written 2 days ago by
Sam • 2.6k
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... If your goal is to filter by MAF of 0.01, then yes. ...
written 2 days ago by
Sam • 2.6k
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... Depends on the algorithm used. If you follow the traditional p-value thresholding approach, then clumping is necessary to avoid bias by LD as suggested by you. However, if they are using more sophisticated models that already accounts for LD e.g. LDpred, lassosum, PRS-CS etc, then they don't need to ...
written 4 days ago by
Sam • 2.6k
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... 1. No. They are of different format
2. if you want to work with the ped file, then you will need to convert them using PLINK. Or you can directly download the data [here][1]
[1]: https://www.cog-genomics.org/plink/1.9/resources ...
written 4 days ago by
Sam • 2.6k
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... I'll usually just read in the data.frame and do the filtering manually myself.
e.g. if my data.frame (`df`) has an INFO column and a MAF column and I want to filter by INFO > 0.8 and MAF > 0.05, I can do
```
res <- subset(df, INFO > 0.8 & MAF > 0.05)
``` ...
written 4 days ago by
Sam • 2.6k
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... Opps, sorry, should be 0.99. Have now edited ...
written 4 days ago by
Sam • 2.6k
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... If that's the case, you will also need to manually install the `digest` package. (can simply use `install.packages("digest")`) ...
written 6 days ago by
Sam • 2.6k
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... Can you confirm that you've successfully install "snpReady"? snpReady seems to be dependent on "impute" which is on Bioconductor instead of CRAN and need to be installed manually with
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocMan ...
written 6 days ago by
Sam • 2.6k
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... If you know the effective allele information, then you can simply filter the effective allele frequency as those > 0.99 and < 0.01. Because if the effective allele frequency is less than 0.01, it's the minor allele. ...
written 6 days ago by
Sam • 2.6k
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