if (args.prev is None): raise Exception('--prev must be supplied')
if (args.pheno is None): raise Exception('--pheno must be supplied')
#Read bfilesim and pheno file for heritability computation
bed, phe = leapUtils.loadData(args.bfilesim,
args.extractSim,
args.pheno,
args.missingPhenotype,
loadSNPs=(args.eigen is None),
standardize=True)
#Read/create eigendecomposition
if (args.eigen is not None): eigen = np.load(args.eigen)
else:
import eigenDecompose
eigen = eigenDecompose.eigenDecompose(bed)
#Compute relatedness
if (args.relCutoff <= 0): keepArr = np.ones(bed.iid.shape[0], dtype=bool)
else:
if (args.related is None):
bed2 = bed
if (args.extractSim is not None or args.eigen is not None):
bed2, _ = leapUtils.loadData(args.bfilesim,
None,
args.pheno,
args.missingPhenotype,
loadSNPs=True)
keepArr = leapUtils.findRelated(bed2, args.relCutoff)
else:
keepArr = leapUtils.loadRelatedFile(bed, args.related)
if (args.extract is not None and args.bfile is None): raise Exception('--extract cannot be used without --bfile')
if (args.bfile is not None and args.resfile is None): raise Exception('--bfile cannot be used without --resfile')
if (args.bfilesim is None): raise Exception('bfilesim must be supplied')
if (args.pheno is None): raise Exception('phenotype file must be supplied')
if (args.out is None): raise Exception('output file name must be supplied')
if (args.prev is None): raise Exception('prevlence must be supplied')
if (args.h2 is None): raise Exception('heritability must be supplied')
#Read bfilesim and pheno file for heritability computation
bed, phe = leapUtils.loadData(args.bfilesim, args.extractSim, args.pheno, args.missingPhenotype, loadSNPs=(args.eigen is None), standardize=True)
#Read/create eigendecomposition
if (args.eigen is not None): eigen = np.load(args.eigen)
else:
import eigenDecompose
eigen = eigenDecompose.eigenDecompose(bed)
#Compute relatedness
if (args.relCutoff <= 0): keepArr = np.ones(bed.iid.shape[0], dtype=bool)
else:
if (args.related is None):
bed2 = bed
if (args.extractSim is not None or args.eigen is not None): bed2, _ = leapUtils.loadData(args.bfilesim, None, args.pheno, args.missingPhenotype, loadSNPs=True)
keepArr = leapUtils.findRelated(bed2, args.relCutoff)
else:
keepArr = leapUtils.loadRelatedFile(bed, args.related)
#Add significant SNPs as fixed effects
covar = None
if (args.resfile is not None):
def eigenDecompose(bed, kinshipFile=None, outFile=None, ignore_neig=False):
import eigenDecompose
return eigenDecompose.eigenDecompose(bed, kinshipFile, outFile,
ignore_neig)
def eigenDecompose(bed, kinshipFile=None, outFile=None, ignore_neig=False): import eigenDecompose return eigenDecompose.eigenDecompose(bed, kinshipFile, outFile, ignore_neig)
def eigenDecompose(bed, outFile=None):
import eigenDecompose
return eigenDecompose.eigenDecompose(bed, outFile)
def eigenDecompose(bed, outFile=None): import eigenDecompose return eigenDecompose.eigenDecompose(bed, outFile)
