Difference between revisions of "Raremetal Incoming updates"
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* In conditional analysis, when cov matrix between the test variant and its conditioned variants is not invertible, MathSVD still tries to invert that matrix and that leads to weird conditional p values. | * In conditional analysis, when cov matrix between the test variant and its conditioned variants is not invertible, MathSVD still tries to invert that matrix and that leads to weird conditional p values. | ||
* '''Optimization for binary traits''' | * '''Optimization for binary traits''' | ||
| + | * '''Memory optimization for gene-based test in large panel''' | ||
Revision as of 08:41, 19 July 2016
Main Wiki Page
Finished in test version
- Optimization for unbalanced studies (Jingjing Yang)
Incoming update
- Add an option to store group file from vcf
- Take snpeff as annotation input
- When no conditional variant is available, warning is generated but not written to log file.
- SKAT conditional analysis misses the last 3 column names. They should be cond_statistics, cond_pvalue_davis, cond_p_value_liu.
- enable reading from .gz annotated vcf
- add SKAT-O
- solve the numeric issue of lambda = 0 in SKAT
- In conditional analysis, when cov matrix between the test variant and its conditioned variants is not invertible, MathSVD still tries to invert that matrix and that leads to weird conditional p values.
- Optimization for binary traits
- Memory optimization for gene-based test in large panel
