owas_clogit: Perform 'omics wide association study for matched case...

In epiomics: Analysis of Omics Data in Observational Studies

Perform 'omics wide association study for matched case control studies

Description

Implements an omics wide association study for matched case control studies using conditional logistic regression. For this function, the variable of of interest should be a dichotomous outcome, and the strata is the variable indicating the matching.

Usage

owas_clogit(
  df,
  cc_status,
  cc_set,
  omics,
  covars = NULL,
  confidence_level = 0.95,
  conf_int = FALSE,
  method = "efron",
  test_data_quality = TRUE
)

Arguments

df	Dataset
cc_status	Name of the variable indicating case control status. Must be either 0/1 or a factor with the first level representing the reference group.
cc_set	Name of the variable indicating the case control set.
omics	Names of all omics features in the dataset reference group.
covars	Names of covariates (can be NULL)
confidence_level	Confidence level for marginal significance (defaults to 0.95, or an alpha of 0.05)
conf_int	Should Confidence intervals be generated for the estimates? Default is FALSE. Setting to TRUE will take longer. For logistic models, calculates Wald confidence intervals via confint.default.
method	method used the correct (exact) calculation in the conditional likelihood or one of the approximations. Default is "efron". Passed to clogit.
test_data_quality	If TRUE (default), then code will ensure that the variance of all variables in the analysis is greater than 0 after dropping any missing data.

Value

A data frame with 6 columns: feature_name: name of the omics feature estimate: the model estimate for the feature. For linear models, this is the beta; for logistic models, this is the log odds. se: Standard error of the estimate test statistic: t-value p_value: p-value for the estimate adjusted_pval: FDR adjusted p-value threshold: Marginal significance, based on unadjusted p-values

epiomics documentation built on April 4, 2025, 1:42 a.m.