relRisk {HLAtools}

Calculate Relative Risk for Individual Alleles and Genotypes in BIGDAWG-formatted Non-Case-Control Datasets

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, save.path = tempdir())

Arguments

dataset

A character string describing the name of a non-case-control genotype dataset using the BIGDAWG format. 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.

save.path

A character string identifying the path in which to write the pair of files when return is FALSE. The default value is tempdir().

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

rr <- relRisk(sHLAdata)