Commit 60f1450f authored by Hanna  JULIENNE's avatar Hanna JULIENNE

Small correction in documentation

parent 4145bf14
Pipeline #11550 passed with stages
in 1 minute and 3 seconds
......@@ -94,6 +94,7 @@ The raiss package outputs imputed GWAS files in the tabular format:
| snp_ids | position | Ref_allele | Alt_allele | z_score | Var | ld_score |
+=============+==========+============+============+=========+=======+==========+
| rs3802985 | 198510 | T | C | 0.334 | -1.0 | -1.0 |
+-------------+----------+------------+------------+---------+-------+----------+
| rs111876722 | 201922 | C | T | 0.297 | 0.16 | 5.412 |
+-------------+----------+------------+------------+---------+-------+----------+
......
......@@ -76,7 +76,7 @@ def z_amplitude_effect(zscore_folder, masked_folder, output_folder, ref_folder,
z_treshold (list) : float list to select Z score to mask above Z score
eigen_ratio (float): rcond parameter (must be between 0 and 1)
window_size, buffer_size, l2_regularization, R2_threshold : imputation parameter (see raiss command line documentation)
N_to_mask (int): Number of SNPs masked in the initial dataset to compute the correlation between true value and imputed value
ratio_to_mask (int): the fraction of SNPs above the z_threshold to mask in the initial dataset to compute the correlation between true value and imputed value
"""
z_file = "{0}/z_{1}_{2}.txt".format(zscore_folder, gwas, chrom)
zscore = pd.read_csv(z_file, index_col=0, sep="\t")
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment