format_gpGeno: Synbreed geno formatting converter

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

Description

Function to convert genotype file from long format to matrix format suitable for Synbreeds gpData object.

Usage

format_gpGeno(data_file, num_ids, num_snps, head = 10, snp_col = 1,
  id_col = 2, allele1_col = 3, allele2_col = 4, format = "doseB")

Arguments

data_file	Path to raw genotyping file in long format
num_ids	Numeric. Number of individuals in file
num_snps	Numeric. Number of SNPs per individual
head	Numeric. Number of header lines.
snp_col	Numeric. Indicates which column in file contains SNP names
id_col	Numeric. Indicates which column in file contains individual names
allele1_col	Numeric. Indicates which column contains genotyping for allele 1.
allele2_col	Numeric. Indicates which column contains genotyping for allele 2.
format	character describing desired output. Options include "doseB", indicating that the output will be in the dosage of allele B format. If doseB is not chosen, output is left in original format.

Value

Genotype matrix with individuals in rows and snps in columns

funkhou9/snpTools documentation built on May 16, 2019, 4:05 p.m.