Commit 7a0985da authored by Hanna  JULIENNE's avatar Hanna JULIENNE

changed toc_tree

parent 31273d62
Pipeline #10227 failed with stage
in 1 minute and 1 second
......@@ -18,7 +18,7 @@ pages:
- cd doc
- sphinx-apidoc -f -o ./source/_autosummary/ ../raiss/
- make html
- mv build/html/ ../public
- mv _build/html/ ../public
artifacts:
paths:
- public
......
......@@ -7,11 +7,13 @@ Welcome to the Robust and Accurate Imputation from Summary Statistics (RAISS) do
============================================================================================
.. toctree::
:caption: Table of Contents
:maxdepth: 2
:caption: Contents:
index
What is RAISS ?
===================
===============
RAISS is a python package to impute missing SNP summary statistics from
neighboring SNPs in linkage desiquilibrium.
......@@ -92,7 +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 |
| rs111876722 | 201922 | C | T | 0.297 | 0.16 | 5.412 |
+-------------+----------+------------+------------+---------+-------+----------+
Command Line Usage
......
"""Module for imputation performance evaluation
Function to generate test dataset with missing SNPs, impute missing SNPs
and compare precision with original dataset.
In other word, this module provides function to empirically measure imputation R2 on independant dataset.
"""
from raiss.pipes import save_chromosome_imputation
import multiprocessing
from joblib import Parallel, delayed
import pandas as pd
import numpy as np
"""
Function to generate test dataset with missing SNPs, impute missing SNPs
and compare precision with original dataset.
In other word, this module provides function to empirically measure imputation R2 on independant dataset.
"""
def generated_test_data(zscore, N_to_mask=5000, condition=None):
"""
......
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