def loadData(bfile,
extractSim,
phenoFile,
missingPhenotype='-9',
loadSNPs=False,
standardize=True):
bed = Bed(bfile)
if (extractSim is not None):
f = open(extractSim)
csvReader = csv.reader(f)
extractSnpsSet = set([])
for l in csvReader:
extractSnpsSet.add(l[0])
f.close()
keepSnpsInds = [
i for i in xrange(bed.sid.shape[0]) if bed.sid[i] in extractSnpsSet
]
bed = bed[:, keepSnpsInds]
phe = None
if (phenoFile is not None):
bed, phe = loadPheno(bed, phenoFile, missingPhenotype)
if (loadSNPs):
bed = bed.read()
if (standardize): bed = bed.standardize()
return bed, phe
def load_data(snp_file, pheno_file, covar_file):
# Load SNP data
snp_reader = Bed(snp_file)
# Load phenotype
pheno = pysnptools.util.pheno.loadPhen(pheno_file)
# Load covariates
if covar_file is not None:
covar = pysnptools.util.pheno.loadPhen(covar_file)
snp_reader, pheno, covar = srutil.intersect_apply([snp_reader, pheno, covar])
covar = covar['vals']
else:
snp_reader, pheno = srutil.intersect_apply([snp_reader, pheno])
covar = None
snp_data = snp_reader.read().standardize()
Y = pheno['vals']
Y -= Y.mean(0)
Y /= Y.std(0)
X = 1./np.sqrt((snp_data.val**2).sum() / float(snp_data.iid_count)) * snp_data.val
K = np.dot(X, X.T) # TODO use symmetric dot to speed this up
assert np.all(pheno['iid'] == snp_data.iid), "the samples are not sorted"
return snp_data, pheno, covar, X, Y, K
def loadData(bfile, extractSim, phenoFile, missingPhenotype='-9', loadSNPs=False, standardize=True): bed = Bed(bfile) if (extractSim is not None): f = open(extractSim) csvReader = csv.reader(f) extractSnpsSet = set([]) for l in csvReader: extractSnpsSet.add(l[0]) f.close() keepSnpsInds = [i for i in xrange(bed.sid.shape[0]) if bed.sid[i] in extractSnpsSet] bed = bed[:, keepSnpsInds] phe = None if (phenoFile is not None): bed, phe = loadPheno(bed, phenoFile, missingPhenotype) if (loadSNPs): bed = bed.read() if (standardize): bed = bed.standardize() return bed, phe
def getChromosome(bfile, chrom):
bed = Bed(bfile)
indsToKeep = (bed.pos[:, 0] == chrom)
bed = bed[:, indsToKeep]
return bed.read().standardize()
def getChromosome(bfile, chrom): bed = Bed(bfile) indsToKeep = (bed.pos[:,0] == chrom) bed = bed[:, indsToKeep] return bed.read().standardize()
def getExcludedChromosome(bfile, chrom):
bed = Bed(bfile)
indsToKeep = bed.pos[:, 0] != chrom
bed = bed[:, indsToKeep]
return bed.read().standardize()
def getExcludedChromosome(bfile, chrom):
bed = Bed(bfile, count_A1=True)
indsToKeep = (bed.pos[:, 0] != chrom)
bed = bed[:, indsToKeep]
return bed.read().standardize()