burdenFirth: Run the burden Firth test

In DavisBrian/Firth: Firth Test

Description

This function runs the burden Firth test.

Usage

burdenFirth(formula, data, Z, snpinfo, aggregateBy = "gene",
  snpNames = "Name", mafRange = c(0, 0.5))

Arguments

formula	an object of class "formula" (or one that can be coerced to that class): a symbolic description of the model to be fitted.The details of model specification are given under 'Details' in the "lm" help file.
data	a data frame, list or environment (or object coercible by as.data.frame to a data frame) containing the variables in the model.
Z	A genotype matrix (dosage matrix) - rows correspond to individuals and columns correspond to SNPs. Use 'NA' for missing values. The row names of this matrix should correspond to the subject names in the phenotype file. The column names of this matrix should correspond to SNP names in the SNP information file.
snpinfo	SNP Info data.frame. Must contain fields given in 'snpName' and 'aggregateBy'
aggregateBy	The column in snpinfo on which the individual snps are to be aggregated by. Default is 'gene'.
snpNames	The column in snpinfo where the SNP identifiers. Defualt is 'Name'
mafRange	Range of MAF's to include in the analysis (endpoints included). Default is all SNPs (0 <= MAF <= 0.5).

Details

This function is a wrapper for the logistf function in the logistf package used in the Firth test.

Value

Results of the burden Firth test.

DavisBrian/Firth documentation built on May 6, 2019, 1:55 p.m.