ldscmod: Function to use LDSC

In georgeg0/iphegwas: Intelligent PheGWAS

Function to use LDSC

Description

Function to use LDSC

Usage

ldscmod(pathname, ldscpath, dentogram = FALSE, plot = FALSE)

Arguments

pathname	The folder that contains the summary stats to use for LDSC
ldscpath	Path to the LDSC GitHub folder in your computer
dentogram	If TRUE returns dentogram using LDSC method
plot	If TRUE returns rg correlation plot using LDSC method

Details

if used for LDSC ordering then summary stats file names should match with the phenos that you are passing to the landscape function.

You should have a ldsc conda environment that you use for running LDSC. Details here https://github.com/bulik/ldsc

Value

Default LDSC ordering/ dentogram is TRUE/ rg plot if TRUE

Author(s)

George Gittu

Examples

## Not run: 
## Giving absolute file path
pathname <- "/Users/ggeorg02/Desktop/databetasefiltered/files_ldsc/"
ldscpath <- "/Users/ggeorg02/Desktop/GitHub/ldsc"
# This gives the order after applying LDSC. We can pass this order to the landscape function
ldscmod(pathname,ldscpath)
ldscmod(pathname,ldscpath,dentogram = TRUE)
ldscmod(pathname,ldscpath,plot = TRUE)

## End(Not run)

georgeg0/iphegwas documentation built on Oct. 15, 2022, 9:53 a.m.