Function to use LDSC

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

Value

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

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

Author

George Gittu

Examples

if (FALSE) {
## 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)
}