Run FImpute from a FImputeRunner object

Source: R/fimpute_runner.R

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{
# Requires the external FImpute3 binary in PATH.
path_fimpute <- file.path(tempdir(), "fimpute_run_example")
param_file <- file.path(path_fimpute, "fimpute.par")

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

runner <- methods::new("FImputeRunner",
                       export    = export_obj,
                       par_file  = param_file,
                       exec_path = "FImpute3")

res <- runFImpute(runner, verbose = TRUE)
} # }