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Dear LCV users,
when using LCV as shown in the tutorial:
LCV = RunLCV(data[,"L2"],data[,"Z.x"],data[,"Z.y"] )
I would often get the error "NaNs produced, probably due to negative heritability est…
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Dear all,
I installed everything. I run the test files. Everything is working.
I created the summary stats based on my summary statistics.
python munge_sumstats.py --sumstats AD_META_GENOTYP…
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Hi ,
I was trying to perform the partitioned heritability calculations. So I took one of your examples, based on the BMI GIANT meta-analysis. (https://github.com/bulik/ldsc/wiki/Partitioned-Herita…
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Dear Dr. Gustavo
The heritability I calculated using BGLR is significantly lower than the heritability reported in the literature. And no errors were reported during the BGLR operation.
The followin…
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I have recently been running a MegaPRS on some meta-analysis summary statistics and using 1000G as a reference panel. This is something I have run earlier this year (prior to version 6) and it worked …
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Dear Team,
I calculated partition heritability for ATAC seq peaks by using 106 GWAS sumstats.
For example: for "PASS.Schizophrenia.Trubetskoy2022 GWAS sumstats", I have 98 categories for peaks. I …
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It work well when single trait is analyzed separately. However it fails when two traits are analyzed together using --rg.
Could you help me figure out it?
Thank you very much!
The details are as …
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Question:
From [docs](https://dougspeed.com/snp-heritability/) it seems like the heritability model need a tagging file? is it possible to do it without?
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I am trying to calculate heritability and getting this error:
Call:
./ldsc.py \
--h2 hearta.sumstats.gz \
--ref-ld-chr aCM/Add_all.chr3 \
--out aCM--print-coefficients \
--overlap-annot \
--f…
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Hi,
Do you have any opinions on whether it is valid to run LDSC (to get the bivariate intercept for DONUTS) when the trait h2 is low?
For our trait we get the following LDSC results (phenotype 1 = …