User: Sam
Sam • 3.0k
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Posts by Sam
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Answer:
A: liftOverPlink Syntax error
... From the look of it, your liftOverPlink.py might be a html file. Could you please make sure you have downloaded the file correctly?
Maybe this link will help
https://github.com/sritchie73/liftOverPlink/archive/master.zip ...
written 5 hours ago by
Sam • 3.0k
2
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1
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... You will need to follow the instruction [here][1] starting from page 8. You will need the md5 password to be able to access the data (which should be attached in an email sent to the PI of the UKB application). After you've got the encrypted data, you can convert it to R format or csv format using u ...
written 7 days ago by
Sam • 3.0k
2
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... Array is for fields that can have multiple entries e.g. ICD10. It is basically breaks down the array into multiple file. For example, if someone has 20 ICD code, then those 20 ICD code will be found in 10 different array files.
Instance is something related to the multiple measurement. Some of the ...
written 8 days ago by
Sam • 3.0k
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... Using data.table (assuming your data is called dt), you can do a t.test on each row with the following code. Though as others have suggested, you should really think about your experimental design and use the appropriate statistic model, otherwise you will just get meaningless p-values.
librar ...
written 9 days ago by
Sam • 3.0k
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1
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... Does that mean you want row 1 compare with all other rows, the repeat? Or are you comparing S1 vs S2, S1 vs S3, ..., S5 vs S6? ...
written 10 days ago by
Sam • 3.0k
1
vote
1
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153
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... Negative beta isn't a problem. you can view effective allele with negative beta as "protective", which is alright. ...
written 13 days ago by
Sam • 3.0k
1
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1
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153
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1
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... You can use the --perm option, which will generate an empirical p-value for you (preferably --perm 10000 or above). If empirical p-value is less than 0.05, then you are good to go. (but do note that the R2 is still inflated as you are not doing out of sample validation) ...
written 14 days ago by
Sam • 3.0k
0
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... The 1000 Genome data can be used as the reference. The usage and requirement for the `--ld` flag is exactly the same as the `--target` flag. You will need the plink or bgen file.
Unfortunately, yes, with your sample size, you will need to think of something clever to have a hope of getting anythin ...
written 14 days ago by
Sam • 3.0k
2
votes
1
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153
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1
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... Your sample size is simply too small. That will usually not give you any reasonable result. I suspect that as you've less than 100 samples, the clumping LD varies quite a lot, lead to more variants being removed than normally would (which lead to the small variant count). One way to get around that ...
written 17 days ago by
Sam • 3.0k
2
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1
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85
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... You can try out [MAGMA][1], which is one of the most popular tool for pathway analysis on GWAS results
[1]: https://ctg.cncr.nl/software/magma ...
written 18 days ago by
Sam • 3.0k
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