genesis2staar_nullmodel: Transforming the null model object fitted using GENESIS to...

In xihaoli/STAARpipeline: STAARpipeline for Analyzing Whole-Genome/Whole-Exome Sequencing Data

Transforming the null model object fitted using GENESIS to the null model object to be used for STAAR

Description

The genesis2staar_nullmodel function takes in the object from fitting the null model using the GENESIS package and transforms it to the object from fitting the null model to be used for STAAR procedure.

Usage

genesis2staar_nullmodel(obj_nullmodel_genesis, use_SPA = FALSE)

Arguments

obj_nullmodel_genesis	an object from fitting the null model, which is the output from fitNullModel function in the GENESIS package.
use_SPA	a logical switch determines if the null model fitting occurs in an imbalanced case-control setting (default = FALSE).

Value

An object from fitting the null model for related samples to be used for STAAR procedure, which is the output from fit_nullmodel function.

References

Gogarten, S.M., Sofer, T., Chen, H., et al. (2019). Genetic association testing using the GENESIS R/Bioconductor package. Bioinformatics, 35(24), 5346-5348. (pub)

Li, X., Li, Z., et al. (2020). Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale. Nature Genetics, 52(9), 969-983. (pub)

Li, Z., Li, X., et al. (2022). A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies. Nature Methods, 19(12), 1599-1611. (pub)

xihaoli/STAARpipeline documentation built on Feb. 9, 2025, 12:39 a.m.