Extract beta, M, and copy-number matrices from a filtered object — extractMetricsMinfiEwasWater • dnaEPICO

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"               
#> [4] "methylationRanges"