From 60f1450f1808873d1615d190230cf3b58b37a871 Mon Sep 17 00:00:00 2001
From: hanna julienne <hanna.julienne@pasteur.fr>
Date: Fri, 26 Apr 2019 10:17:45 +0200
Subject: [PATCH] Small correction in documentation
---
doc/source/index.rst | 1 +
raiss/imputation_R2.py | 2 +-
2 files changed, 2 insertions(+), 1 deletion(-)
diff --git a/doc/source/index.rst b/doc/source/index.rst
index 27a73a3..0def135 100644
--- a/doc/source/index.rst
+++ b/doc/source/index.rst
@@ -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 |
+-------------+----------+------------+------------+---------+-------+----------+
diff --git a/raiss/imputation_R2.py b/raiss/imputation_R2.py
index d4569e9..ca9daf0 100644
--- a/raiss/imputation_R2.py
+++ b/raiss/imputation_R2.py
@@ -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")
--
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