Deprecated: Use of this version of MAPIT is deprecated. More information on our Applications Support and Retention Policy.Epistasis, commonly defined as the interaction between multiple genes, is an important genetic component underlying phenotypic variation. Many statistical methods have been developed to model and identify epistatic interactions between genetic variants. However, because of the large combinatorial search space of interactions, most epistasis mapping methods face enormous computational challenges and often suffer from low statistical power. In Crawford et al. (2017) and Crawford and Zhou (2018), we present a novel, alternative strategy for mapping epistasis: the MArginal ePIstasis Test (MAPIT). Our method examines one variant at a time, and estimates and tests its "marginal epistatic effects" --- the combined pairwise interaction effects between a given variant and all other variants. By avoiding explicitly searching for interactions, our method avoids the large combinatorial search space and improves power. Our method is novel and relies on a recently developed variance component estimation method for efficient and robust parameter inference and p-value computation.
Accessing MAPIT d0b348a-foss-2018b-R-3.5.1
To load the module for MAPIT d0b348a-foss-2018b-R-3.5.1 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):
module load MAPIT/d0b348a-foss-2018b-R-3.5.1
BEAR Apps Version
EL8-cascadelake — EL8-haswell — Ubuntu20.04-haswell
The listed architectures consist of two part: OS-CPU.
- BlueBEAR: The OS used on BlueBEAR is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.
- BEAR and CaStLeS Cloud VMs: These VMs can have one of two OSes. Those with access to a BEAR Cloud or CaStLeS VM should check that the listed architectures for an application include the OS of VM being used. The VMs, irrespective of OS, will use the haswell CPU type.
For more information visit the MAPIT website.
This version of MAPIT has a direct dependency on: foss/2018b R/3.5.1-foss-2018b truncnorm/1.0-8-foss-2018b-R-3.5.1
Last modified on 5th June 2019