read.findhap is a tool that utilizes external C code to read quickly the output of
findhap program stored by default in the ‘genotypes.filled’ file. ‘findhap’
is a standalone software program written by Paul Vanraden to impute missing genotypes. If you
are not familiar with ‘findhap’, you probably don't need this function.
read.findhap(Nanim, Nmark, file="./genotypes.filled")Total number of individuals to read from imputed genotypes file.
Total number of SNP genotypes in the imputed-to chip.
Findhap's output file for imputed genotypes. Default is ‘genotypes.filled’.
An object of class matrix with ‘number of rows = Nanim’ and ‘number of columns = Nmark + 3’. Refer to findhap manual for more details about the structure of ‘genotypes.filled’.
This function reads into R environment imputed SNP genotypes as formated by findhap program. This tool utilizes external C code for quick read. The standard output of this function is an object of class matrix.
Paul Vanraden. Find haplotypes and impute genotypes using multiple chip sets and sequence data. http://aipl.arsusda.gov/software/findhap/.