singlesnpFirth: Run the single snp Firth test

In DavisBrian/Firth: Firth Test

Description

This function runs the single snp Firth test.

Usage

singlesnpFirth(formula, data, Z, snpinfo = NULL, snpNames = NULL,
  refCol = NULL, altCol = NULL)

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	(optional) SNP Info data.frame. See Details.
snpNames	(optional) The column in snpinfo where the SNP identifiers are found. See Details.
refCol	(optional) The column in snpinfo where the reference allele for the SNP identifier is found. See Details.
altCol	(optional) The column in snpinfo where the alternate allele for the SNP identifier is found. See Details.

Details

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

Value

Results of the Firth test in a RAREMETAL friendly format.

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