Closed Al-Murphy closed 3 years ago
Been a while since i used LDSC but im sure i could figure it out. Will add to my branch (bschilder_dev) once I do.
Great, let me know if I can help with this? I have yet to actually run LDSC myself though!
Info here: https://github.com/bulik/ldsc/wiki/Summary-Statistics-File-Format
I think we have most things by default except:
That said, Kitty was able to run Open GWAS sum stats i just processed with MungeSumstats, but only after running LDSC's munge_sumstats.py
https://github.com/bulik/ldsc/blob/master/munge_sumstats.py
Yep so Roxy said a similar thing that after running munge_sumstats.py it was fine. We should probably look at that function? My interpretation was that it just removed unnecessary columns?
Exporting to LDSC format is now supported by setting format_sumstats(ldsc_format=TRUE, ...)
New functions to support this are:
https://github.com/neurogenomics/MungeSumstats/blob/bschilder_dev/R/check_ldsc_format.R
https://github.com/neurogenomics/MungeSumstats/blob/bschilder_dev/R/check_zscore.R
Passed force_new_z
up to format_sumstats
and set default to FALSE.
@bschilder might be worth us looking into adding this functionality to your branch, it was asked for from a user. Do you know what exactly is required for this format?