Description Usage Arguments Details Value
This function runs the burden Firth test.
1 2 | burdenFirth(formula, data, Z, snpinfo, aggregateBy = "gene",
snpNames = "Name", mafRange = c(0, 0.5))
|
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). |
This function is a wrapper for the logistf function in the logistf package used in the Firth test.
Results of the burden Firth test.
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