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Commits (2)
......@@ -14,7 +14,7 @@ def launch_chromosome_imputation(args):
args (dict): Argument parsed from the command line see the
__main__.add_chromosome_imputation_argument(parser) function.
"""
save_chromosome_imputation(args.gwas, args.chrom, args.window_size, args.buffer_size, args.l2_regularization, args.eigen_threshold, args.zscore_folder, args.ref_folder, args.R2_threshold)
save_chromosome_imputation(args.gwas, args.chrom, args.window_size, args.buffer_size, args.l2_regularization, args.eigen_threshold, args.zscore_folder, args.ref_folder, args.ld_folder, args.output_folder, args.R2_threshold)
def add_chromosome_imputation_argument():
......
......@@ -81,7 +81,7 @@ def z_amplitude_effect(zscore_folder, masked_folder, output_folder, ref_folder,
def run_imputation(z, i):
print("Z score threshold : {}".format(z))
condition = (dat_orig.Z > z)
condition = (dat_orig.Z.abs() > z)
print("Number of SNPs verifying condition : {}".format(condition.sum()))
N_to_mask = np.int(np.floor(condition.sum()*0.5))
......
......@@ -6,7 +6,7 @@ setup(name='raiss',
url='https://gitlab.pasteur.fr/statistical-genetics/raiss',
author='Hanna Julienne',
author_email='hanna.julienne@pasteur.fr',
install_requires = ['scipy', "pandas"],
install_requires = ['scipy', "pandas", "joblib"],
license='MIT',
#package_dir = {'': 'jass_preprocessing'},
packages= ['raiss'],
......