fimpute_run: Run Fimpute
In funkhou9/snpTools: Miscellaneous tools for working with SNP genotyping data

Invoke Fimpute for imputation and genotype phasing from within R. Uses R objects for genotypes, maps, and pedigrees to construct Fimpute inputs, and executes an Fimpute run. Fimpute is required to be on your PATH, or otherwise specify the location of the Fimpute binary with the path argument

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fimpute_run(geno, map, ped = NULL, path = NULL, groups = NULL,
  exclude_chr = NULL, output_folder = getwd(), parent = FALSE,
  reference = FALSE, keep_fimpute = FALSE)

`geno`	a matrix or data.frame with SNPs in columns and individuals in rows. Genotypes must be coded as dosage of allele 'b' 0, 1, 2.
`map`	a data.frame containing SNP map information for each SNP present in geno
`ped`	a data.frame pedigree providing family information for each individual in geno. The first column of the pedigree is for ID, second is for sire/father ID, third is for dam/mother ID, fourth is sex of ID "M" or "F". If ids in geno are not present in pedigree, they will be added to the end with missing parent information and a "M" sex. Correct sex information should only be required when imputing/phasing the sex chromosomes.
`path`	a character represting the path to the FImpute binary. If omitted, assumes FImpute binary resides along PATH.
`groups`	a list of character vectors with the names of IDs meant to be processed as groups. Names of list should be the names of the groups, with each element containing IDs.
`exclude_chr`	a character vector of chromosomes to exclude
`output_folder`	a character providing the location of desired FImpute output
`parent`	logical use TRUE if only parents identified from the pedigree are to be reference animals
`reference`	logical use TRUE if you want 'groups' to be used to specify the reference animals used by FImpute. Not compatable with parent TRUE
`keep_fimpute`	logical use TRUE to remove associated files used to run FImpute.