Heterogametic_Genotype_Warnings: Heterogametic warnings

In genotypeR: SNP Genotype Marker Design and Analysis

Description

Heterogametic_Genotype_Warnings provides QA for back cross designs by determine those organisms that have an impossible genotypes based on their sex.

Usage

Heterogametic_Genotype_Warnings(seq_data, sex_chromosome, sex_vector,
  heterogametic_sex)

Arguments

seq_data	is genotyping data read in with read_in_sequenom_data
sex_chromosome	character of the sex chromosome coded in sequenom markers produced with make_marker_names. For example, the sex chromosome in the data provided with genotypeR is chrXL and it has been coded as chrXL_start_end. The character provided would be "chrXL"
sex_vector	a vector of the sex of each individual in seq_data coded the same as that in heterogametic sex. For example, a vector of "F" and "M".
heterogametic_sex	character of heterogametic sex (e.g., "M")

Value

A data frame of warnings

Examples

data(genotypes_data)
seq_data <- genotypes_data
sex_vector <- do.call(rbind, strsplit(seq_data[,"SAMPLE_NAME"], split="_"))[,2]
Heterogametic_Genotype_Warnings(seq_data=seq_data, sex_chromosome="chrXL",
sex_vector=sex_vector, heterogametic_sex="M")

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