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Hello!
I'm planning to use GAPIT for GWAS data analysis. However, my phenotype data is categorical, while the models provided by GAPIT are based on numerical data.
The GAPIT manual mentions that…
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Hi,
I`m new in this field and not good at the mathematics.
Recently I`m doing two sample MR analysis between metabolome sumstats by using MRlap. I found most of my results have extremely large …
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library(vroom)
library(textshape)
library(plyr)
library(dplyr)
library(sommer) #Version 4.1
Sys.setenv("VROOM_CONNECTION_SIZE" = "13200000")
options(expressions = 5e5)
#READ IN TABLES
phen…
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Hi,
I am running ldsc with two summary statistics of trait1 and proxy for trait1 with completely non-overlapping european study samples (N1 = 900k (publishded meta-analysis), N2 = 180k (one sample…
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I want to compute LDSC heritability and genetic correlation of a genome-wide meta-analysis including repeated observations and I was wondering what value for sample size I should use.
For example,…
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Hi,
I am trying to run the partition heritability functionality with my own annotations. I managed to reproduce your results from Finucane 2015, on the Cahoy annotations. I was wondering if you coul…
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Hi I have an issue referencing supplementary figures in the below code
This is how the figure environment is defined
```\begin{figure}
\includegraphics{fig2.pdf}
\caption{
Illustration …
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Hi,
Before i used MTAG, i used LDSC and tried to calculate the genetic correlation of two traits. However, at the first step of LSDC, in the log of one trait showed that "WARNING: mean chi^2 may be…
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-[] Describe Figure 2, I have to set up the question.(Not a report to say what I have done, just say why I have done it).
-[p] literature gene finding
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Hi,
I am using the ldsc.py with the h2 option to estimate heritability on case-control summary statistics.
It seems I have almost no polygenicity signal. Can you help me with interpreting this?
I …