eGene-MVN¶
Description¶
eGene-MVN is an efficient and accurate multivariate normal sampling (MVN) approach to perform the multiple testing correction in eQTL studies. As the above figure shows, we first find a SNP with the minimum p-value among all SNPs in cis with a gene. We then perform multiple testing correction using our MVN approach to correct this p-value. This correct p-value is "eGene" p-value for this gene. Our approach is more than 100 times faster than the permutation test when sample size is 2,000. When sample size is small such as 70, our method is still at least 25 times faster than the permutation test. Our algorithm uses two scaling algorithms to make MVN approach have similar eGene p-values as those from the permutation test.
Environment Modules¶
Run module spider egene-mvn to find out what environment modules are available for this application.
Environment Variables¶
- HPC_EGENE_MVN_DIR - installation directory
- HPC_EGENE_MVN_BIN - executable directory
- HPC_EGENE_MVN_FPR - fpr directory
- HPC_EGENE_MVN_EXE - examples directory
- HPC_EGENE_MVN_PVAL - pval directory
Citation¶
If you publish research that uses egene-mvn you have to cite it as follows:
Categories¶
biology, genomics