Prepare phenotype-plus-beta data for one-timepoint GLM analyses — prepareMethylationGLM

Load the merged phenotype-plus-beta input object, validate the requested modeling variables, convert selected variables to factors, and return a single in-memory object for downstream helpers.

prepareMethylationGLM_T1Data(
  inputPheno,
  phenotypes,
  covariates,
  factorVars,
  cpgPrefix = "cg",
  cpgLimit = NA,
  interactionTerm = NULL,
  prsMap = NULL,
  verbose = FALSE,
  logs = FALSE,
  log_dir = NULL,
  log_file = "log_methylationGLM_T1.txt"
)

Arguments

inputPheno: Character. Path to the merged phenotype-plus-beta object created by preprocessingPheno().
phenotypes: Character vector or comma-separated string of phenotype variables to model.
covariates: Character vector or comma-separated string of covariate variables to adjust for.
factorVars: Character vector or comma-separated string of variables that should be converted to factors before modeling.
cpgPrefix: Character. Prefix used to identify methylation columns.
cpgLimit: Integer or NA. Maximum number of CpGs to retain. NA keeps all matching CpGs.
interactionTerm: Character or NULL. Optional interaction term.
prsMap: Character vector or comma-separated string of phenotype-to-PRS mappings in the form "Phenotype:PRS".
verbose: Logical. If TRUE, emit progress messages with message().
logs: Logical. If TRUE, write the same messages to a log file.
log_dir: Character or NULL. Directory used for the log file when logs = TRUE.
log_file: Character. File name used when logs = TRUE.

Value

A list with class "dnaEPICO_methylationGLM_T1_data" containing the prepared analysis data, parsed variable selections, CpG columns, and exploratory summaries.

Examples

ex <- dnaEPICO:::exampleMethylationGLMStateDnaEpico()
prepared_data <- prepareMethylationGLM_T1Data(
  inputPheno = ex$inputPath,
  phenotypes = "status",
  covariates = "sex,age",
  factorVars = "status,sex",
  cpgLimit = 2,
  verbose = FALSE,
  logs = FALSE
)
names(prepared_data)
#>  [1] "data"                     "phenotypes"              
#>  [3] "covariates"               "factorVars"              
#>  [5] "cpgColumns"               "cpgPrefix"               
#>  [7] "cpgLimit"                 "prsMap"                  
#>  [9] "interactionTerm"          "requestedInteractionTerm"
#> [11] "missingCounts"            "variableSummary"         
#> [13] "interactionTable"