initialize_genotypeR_data: initialize_genotypeR_data; must provide warning allele

In genotypeR: SNP Genotype Marker Design and Analysis

Description

This initializes the genotypeR data structure used throughout the package.

Usage

initialize_genotypeR_data(seq_data, genotype_table, warning_allele = "Ref",
  output = "pass_through")

Arguments

seq_data	is a data frame of genotyping data
genotype_table	data frame produced with Ref_Alt_Table
warning_allele	is the impossible allele for a BC design taking the value "Ref" or "Alt"
output	this can take 3 values: 1) "warnings" which returns a data frame of BC warnings, 2) "warnings2NA" which returns a genotyping data frame where the warnings have been converted to NAs, or "pass_through" which returns a data frame that is unchanged (default).

Value

A genotypeR object

Examples

data(genotypes_data)
data(markers)
## genotype table
marker_names <- make_marker_names(markers)
GT_table <- Ref_Alt_Table(marker_names)
## remove those markers that did not work
genotypes_data_filtered <- genotypes_data[,c(1, 2, grep("TRUE",
colnames(genotypes_data)%in%GT_table$marker_names))]

warnings_out2NA <- initialize_genotypeR_data(seq_data = genotypes_data_filtered,
genotype_table = GT_table, output = "warnings2NA")

genotypeR documentation built on May 2, 2019, 8:25 a.m.