rebet: The subREgion-based BurdEn Test (REBET)

In REBET: The subREgion-based BurdEn Test (REBET)

Description

A Subregion-based Burden Test for Simultaneous Identification of Susceptibility Loci and Sub-regions within

Usage

 rebet(response, genotypes, subRegions, responseType=NULL, 
        covariates=NULL, shape1=1, shape2=1, saveMem=FALSE)

Arguments

response	Numerical vector of phenotypes. A binary phenotype must be coded as 0 and 1.
genotypes	Matrix of genotypes with each column as a locus.
subRegions	Sub-region annotation vector with length equal to the number of columns of genotypes. In the returned object, these regions will appear as paste("Region_", subRegions, sep="").
responseType	NULL, "continuous" or "binary". If NULL, then "continuous" or "binary" will be chosen based on Y. The default is NULL.
covariates	NULL or matrix of covariates. The default is NULL.
shape1	The shape1 parameter in the beta distribution. The default is 1.
shape2	The shape2 parameter in the beta distribution. The default is 1.
saveMem	TRUE or FALSE to conserve memory (see details). The default is FALSE.

Details

See the reference for details of this method.

Missing values in any of response, genotypes or covariates will be removed before the analysis. Setting saveMem to TRUE will allow for the analysis of a much larger number of subjects, but will take more time to compute. When saveMem is FALSE, there needs to be enough memory available to hold two or three NxN matrices, where N is the number of subjects.

This function calls the h.traits function in the ASSET package.

Value

The object returned from h.traits in the ASSET package.

Author(s)

Bin Zhu <[e-mail]>, Lisa Mirabello and Nilanjan Chatterjee

References

Zhu, B., Mirabello, L., Chatterjee, N. (2018) A Subregion-based Burden Test for Simultaneous Identification of Susceptibility Loci and Sub-regions within Genetic Epidemiology. In press. https://doi.org/10.1002/gepi.22134

Examples

  data(data, package="REBET")

  res <- rebet(response, genotypes, subRegions)
  h.summary(res)

REBET documentation built on Nov. 8, 2020, 8:27 p.m.