Run impute on the specified inputfile

This function runs impute across the input using the specified region.size.

run.impute(
  inputfile,
  outputfile.prefix,
  is.male,
  imputeinfofile,
  impute.exe = "impute2",
  region.size = 5000000,
  chrom = NA,
  seed = as.integer(Sys.time())
)

Arguments

inputfile

Full path to a csv file with columns: Physical.Position, Allele.A, Allele.B, allele.frequency, id ,position, a0, a1

outputfile.prefix

Prefix to the output file. Region boundaries are added as suffix.

is.male

Boolean describing whether the sample is male (TRUE) or female (FALSE)

imputeinfofile

Path to the imputeinfofile on disk.

impute.exe

Pointer to where the impute2 executable can be found (optional).

region.size

An integer describing the region size to be used by impute (optional).

chrom

The name of a chromosome on which this function should run (names are used, supply X as 'X') (optional).

seed

The seed to be set

Author

dw9