Most statistical tests (except for EMMAX) are implemented in R.Core input/output routines are implemented in C++.Integrative and versatile framework that allows easy addition of additional statistical test.Parallel run of job is simply adding one parameter when running EPACTS.Makefile-based partition into and ligation of multiple subtasks.See the "Currently Supported Statistical Tests" section below for more information.Supports a large number of widely used statistical tests for single variant association and burden tests.Utilize PED format to perform test across multiple traits.Support for using genotype dosages instead of hard genotype calls.Support selecting markers by arbitrary combination of substring matching.Efficient library for accessing VCF file to reduce computational burden to analyze large-scale sequencing data.Robust support for widely used format of sequence-based genotypes (VCF) and phenotypes with pedigree (PED).Added emmax-SKAT (contributed by Seunngeun Lee)ĮPACTS currently provides the following set of key features.Fixed errors in SKAT-O (thanks to Anubha Mahajan and Jason Flannick).Fixed errors in loading the dynamic library.Fixed an error which occasionally report mismatches in the number of samples.Relaxed the checking of low-rank matrix in SKAT tests (to avoid unncessary skipping of genes).Fixed a number of minor bugs (more comprehensive fix is still pending).EMMAX-SKAT is implemented with major bug fix.Some major fixes in handling large sample size (>18,000).Please join in the EPACTS Google Group to ask / discuss / comment about EPACTS. 11 Implementing Additional Statistical Tests.8.2 PED file for Phenotypes and Covariates.7.4.2 Burden-style EMMAX Association Analysis.7.4.1 Single Variant EMMAX Association Analysis.7.4 Specialized Instruction for EMMAX tests.7.3 Gene-wise or group-wise burden test.7.2.4 Manhattan Plot of Test Statistics.7.2.3 Q-Q plot of test statistics (stratified by MAF).7.2.1 Output Text of All Test Statistics.5 Currently Supported Statistical Tests.
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