Write the merged phenotype plus cell-composition table

writePhenoLCMinfiEwasWater(
  lcData,
  file,
  verbose = FALSE,
  logs = FALSE,
  log_dir = NULL,
  log_file = "log_writePhenoLCMinfiEwasWater.txt"
)

Arguments

lcData: Object returned by estimateLCMinfiEwasWater().
file: Character. Path to the CSV file to write.
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

Invisibly returns file.

Examples

ref_file <- system.file("extdata", "saliva.txt", package = "dnaEPICO")
beta <- as.matrix(utils::read.table(ref_file))[1:20, , drop = FALSE]
colnames(beta) <- c("sample1", "sample2")
targets <- data.frame(
  Sample_Name = colnames(beta),
  Timepoint = c("T1", "T2"),
  stringsAsFactors = FALSE
)
lc_data <- estimateLCMinfiEwasWater(
  beta = beta,
  targets = targets,
  lcRef = "saliva",
  phenoOrder = "Sample_Name;Timepoint"
)
output_file <- file.path(tempdir(), "phenoLC.csv")
writePhenoLCMinfiEwasWater(lcData = lc_data, file = output_file)
file.exists(output_file)
#> [1] TRUE