Extract beta, M, and copy-number matrices from a filtered object

Extract beta, M, and copy-number matrices from a filtered object

extractMetricsMinfiEwasWater(
  filteredData,
  verbose = FALSE,
  logs = FALSE,
  log_dir = NULL,
  log_file = "log_extractMetricsMinfiEwasWater.txt"
)

Arguments

filteredData

Object returned by filterProbesMinfiEwasWater().

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_metrics" containing beta, m, and cn.

Examples

ex <- dnaEPICO:::exampleMinfiMetricsStateDnaEpico()
metrics_data <- extractMetricsMinfiEwasWater(
  filteredData = ex$filteredData,
  verbose = FALSE,
  logs = FALSE
)
names(metrics_data)
#> [1] "beta" "m"    "cn"