relRisk: Calculate Relative Risk for Individual Alleles and Genotypes...

In sjmack/BDRR: Calculate Relative Risk for BIGDAWG-formatted Genotype Data

Description

This function returns a list object containing relative risk, confidence interval and p-value data for the individual alleles and individual genotypes at each locus in a BIGDAWG-formatted non-case-control genotype data frame or file.

Usage

relRisk(dataset, return = TRUE)

Arguments

dataset

The name of a BIGDAWG formatted non-case-control genotype dataset. Here, "non-case-control" means that while two subject categories are required, the categories should not be patients and controls; instead, the categories may be, e.g., for a dataset of patients, either of two disease states, where one disease state is coded as 0 and the other is coded as 1 in the second column of the dataset. Either a tab-delimited file or a data frame can be specified.

return

A logical identifying if the list object should be returned (return=TRUE), or if pairs of tab-delimited text files of results (one for alleles and one for genotypes) should be written to the working directory for each locus.

Value

A list object of two lists ("alleles" and "genotypes"), each of which contains a list of nine-column data frames containing results for each unique allele or genotype (in rows) at each locus. Column headers in each dataframe are, *Locus*, *Variant*, *Status_1*, *Status_0*, *RelativeRisk*, *CI.low*, *CI.high*, *p.value*, and *Significant*.

References

BIGDAWG Data Format

Examples

# Analyzing the BIGDAWG::HLA_data dataset 
library(BIGDAWG)
rr <- relRisk(HLA_data[,1:4])

sjmack/BDRR documentation built on May 17, 2020, 12:25 a.m.