Predict biological sex from a filtered raw-data object — predictSexMinfiEwasWater • dnaEPICO

Predict sample sex from a genome-mapped methylation object, align the predictions with phenotype data, and return a structured object that can be plotted or merged into downstream phenotype tables.

predictSexMinfiEwasWater(
  rawData,
  targets,
  SampleID = "Sample_Name",
  sexColumn = "Sex",
  verbose = FALSE,
  logs = FALSE,
  log_dir = NULL,
  log_file = "log_predictSexMinfiEwasWater.txt"
)

Arguments

rawData: Object returned by buildRawMinfiEwasWater().
targets: Filtered phenotype data frame aligned with rawData.
SampleID: Character. Name of the sample identifier column in targets.
sexColumn: Character. Name of the phenotype column containing reported sex.
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_minfiEwasWater_sex" containing the sex prediction result, aligned phenotype data, plotting data, and mismatch table.

Examples

ex <- dnaEPICO:::exampleMinfiWorkflowStateDnaEpico()
sex_data <- predictSexMinfiEwasWater(
  rawData = ex$rawFiltered,
  targets = ex$sampleData$targets,
  SampleID = "Sample_Name",
  sexColumn = "Sex",
  verbose = FALSE,
  logs = FALSE
)
names(sex_data)
#> [1] "pSex"        "targets"     "sexPlotData" "mismatches"  "SampleID"   
#> [6] "sexColumn"