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Hi,
I am using LDpred to calculate PRS socres, but encountered the following error.
```shell
$ python ${workdir}/LDpred.py --debug score --gf=${input1}/chr22 --rf=/home/chenf/WJ/PRS_20190807/R…
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Sometimes when calculating polygenic risk scores variants are "skipped due to a mismatching allele code", i.e. where the variant in the input genotype file has allele codes from the opposite strand to…
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I'd like to run the `LDpred.py` script as described in the documentation but running `pip install ldpred` (with or without the `--user` flag) does not install anything called `LDpred.py` anywhere, whi…
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Hi Michel,
Genomic SEM is an amazing resource. Fantastic work and congrats to the whole team. I have a specific question. I'll take the example from the paper itself. If I'd like to generate a sum…
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Hi Sam,
I have tried to run PRSet using the version 2.2.10 on my data and despite it gives me a summary, the p-competitive remains the same across > 2000 pathways. Also, the coefficient seems to be…
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Following along the vignette entitled "Computing polygenic scores using Stacked Clumping and Thresholding (SCT)" everything works until the function snp_grid_PRS. The problem is mismatched dimensions…
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Following previous issue #30
I am using BGEN and I am having the same issue:
6330995 variant(s) observed in base file, with:
6330995 variant(s) not found in target file
0 total variant(s) inc…
ghost updated
5 years ago
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Hi,
I am trying to test what is the minimum read coverage that can still be considered identifying information for a sample, starting by testing my own data.
I *could* successfully identify my o…
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Hi, PRSice2 looks like a very useful program. But i’m not sure whether it can be used to just characterise individuals in terms of an existing polygenic risk score ? i.e. i want to characterise indivi…
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Hi Bjarni,
Sorry for bothering you again.
I have question in how to select the best risk sore from the seven output files (1,0.01,0.03.....0.003).
I count the number of non-zero effect sites an…