read.findhap: Read the output of Paul Vanraden's findhap,...

In gdmp: Genomic Data Management

Description

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.

Usage

read.findhap(Nanim, Nmark, file="./genotypes.filled")

Arguments

Nanim	Total number of individuals to read from imputed genotypes file.
Nmark	Total number of SNP genotypes in the imputed-to chip.
file	Findhap's output file for imputed genotypes. Default is ‘genotypes.filled’.

Details

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.

Value

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’.

References

Paul Vanraden. Find haplotypes and impute genotypes using multiple chip sets and sequence data. http://aipl.arsusda.gov/software/findhap/.

gdmp documentation built on May 1, 2019, 8:07 p.m.