434c2749b0b3da4806786f1feb5ea03e83ff7db6,munge_sumstats.py,,process_n,#Any#Any#Any#,256

Before Change

		dat = dat[dat.N >= n_min]
		
	if "NSTUDY" in dat.columns and "N" in dat.columns:
		dat.drop(["NSTUDY"], inplace=True, axis=1)
	elif "NSTUDY" in dat.columns and "N" not in dat.columns:
		nstudy_min = args.nstudy_min if args.nstudy_min else dat.NSTUDY.max()
		dat = dat[dat.NSTUDY >= nstudy_min].drop(["NSTUDY"], axis=1)
		

After Change

	
	if "N" in dat.columns:
		n_min = args.n_min if args.n_min else dat.N.quantile(0.9) / 1.5
		old = len(dat)
		dat = dat[dat.N >= n_min].reset_index(drop=True)
		new = len(dat)
		log.log("Removed {M} SNPs with N < {MIN} ({N} SNPs remain).".format(M=old-new, N=new, MIN=n_min))
		

Instances