run.impute: Run impute on the specified inputfile

In Wedge-lab/battenberg: Battenberg subclonal copy number caller

Run impute on the specified inputfile

Description

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

Usage

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(s)

dw9

Wedge-lab/battenberg documentation built on July 31, 2023, 1:32 p.m.