@@ -6,16 +6,38 @@ you can generate analysis for any combination
and several joint tests with the command jass create-project-data
(see command line usage for the detail of arguments).
Whatever the test used, the command will generate three output:
Genome-wide analysis
--------------------
Whatever the test used, the command will generate three main output:
* A HDFStore containing several tables (Each table can be read from the HDFStore with the pandas.read_hdf function):
- 'SumStatTab' : The results of the joint analysis by SNPs
- 'PhenoList' : the meta data of analysed GWAS
- 'COV' : The H0 covariance used to perform joint analysis
- 'Regions' : Results of the joint analysis summarised by LD regions
- 'SumStatTab' : The results of the joint analysis by SNPs
- 'PhenoList' : the meta data of analysed GWAS
- 'COV' : The H0 covariance used to perform joint analysis
- 'Regions' : Results of the joint analysis summarised by LD regions
* A .png Manhattan plot
* A .png Quadrant plot which is a scatter plot of the minimum p-value by region of the joint test with respect to the minimum p-value by region of the univariate tests.
You can also get:
- The multi-phenotype analysis results file in CSV format,
- A png image of the quantile-quantile plot (qq-plot) that shows the validity of the results by comparing the distribution of SNP results to the theoretical distribution.
Analysis by region
------------------
To perform an analysis by region (local analysis) you must give the chromosome number and the start and end of the region to be studied.
Whatever the test used, the command will generate three output:
* A HDFStore containing several tables (Each table can be read from the HDFStore with the pandas.read_hdf function):
- 'SumStatTab' : The results of the joint analysis by SNPs for the interval [start-end] chosen by the user
- 'PhenoList' : the meta data of analysed GWAS
- 'COV' : The H0 covariance used to perform joint analysis
- 'Regions' : Results of the joint analysis summarised by LD regions (only for the interval [start-end] chosen by the user)
- 'gene_exon' : Genes label, start and end position, direction, biotype. Exons label, start and end position, associated gene. (the genes and exons data are available only for the interval [start-end] chosen by the user)
* A .png zoom plot (Manhattan plot restricted to the interval [start-end] chosen by the user)
* The multi-phenotype local analysis results file in CSV format
