Run FImpute from a FImputeRunner object — runFImpute • SNPtools

This function runs the external FImpute software using a `FImputeRunner` object, ensuring that all required input files are present and the results are imported.

runFImpute(object, verbose = TRUE)

# S4 method for class 'FImputeRunner'
runFImpute(object, verbose = TRUE)

Arguments

object: An object of class `FImputeRunner`.
verbose: Logical. If TRUE (default), FImpute output will be printed to the console.

Value

An updated `FImputeRunner` object with the `results` slot populated (SNPDataLong).

Examples

if (FALSE) { # \dontrun{
# Example: Running FImpute from a FImputeRunner object

path_fimpute <- "fimpute_run_example"
param_file <- file.path(path_fimpute, "fimpute.par")
fimpute_exec <- "FImpute3"  # assuming it is in PATH

export_obj <- new("FImputeExport",
                  geno = geno_obj@geno,
                  map = geno_obj@map,
                  path = path_fimpute)

runner <- new("FImputeRunner",
              export = export_obj,
              par_file = param_file,
              exec_path = fimpute_exec)

runner <- runFImpute(runner, verbose = TRUE)
head(runner@results@geno)
} # }