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Hello,
Does the current PheWAS package support dosage input (instead of 0,1,2 genotypes)? If not, are you planning to include this in the future?
Currently, when I give dosage information as gen…
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Hi,
Thanks for your great efforts in developing and maintaining LDpred.
I get the error message below repeatedly when I try to run `ldpred`.
`ldpred --coord=/data1/ishim/GRS/coord --ld_radius…
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Hello,
I have completed the first two stages of LDRED - coord_genotypes.py & LDpred.py. These have generated a number of files
_coord.hdf5
ldpred_LDpred-inf.txt
....
LDpred_p1.0000e+00.txt
…
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Hi,
Not so much an issue, rather some questions regarding genotypes of the validation data.
From your explanation in the Readme I deduce that one can only use hard-coded genotypes? So I have to …
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Unsure of what to call this - polygenic score, polygenic risk score? What reference?
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I would like to include SparSNP in a comparison of statistical methods for computing polygenic risk scores.
In the documentation, you show how to perform a cross-validation, but I didn't find how to …
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I'm trying to run LD regression and have been following the tutorial on here https://github.com/bulik/ldsc/wiki/Heritability-and-Genetic-Correlation
I have downloaded python and required packages th…
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Hi,
I am using the LD Score Regression method to compute the genetic correlation between two different phenotypes in patients from European ancestry (using summary statistic data). I have noticed so…
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Hello,
For a series of phenotypes I'm getting Ratio values of 17% and even 30%. The GWAS data is not genomic-controlled. However, when I tried a GC version of the same analyses, the results were not m…
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This should have a parameter that specifies the number of models to return by rank (default to 10). Because we have several scoring mechanisms, this will default to just one of them (maybe BMAasymIC)…