BIGr (version 0.6.2)

flip_dosage: Switch Dosage Values from a Genotype Matrix

Description

This function converts the dosage count values to the opposite value. This is primarily used when converting dosage values from reference based (0 = homozygous reference) to alternate count based (0 = homozygous alternate). It assumes that the Samples are the columns, and the genomic markers are in rows. Missing data should be set as NA, which will then be ignored for the calculations. All samples must have the same ploidy.

Usage

flip_dosage(df, ploidy, is.reference = TRUE)

Value

A genotype matrix

Arguments

df

Genotype matrix or data.frame

ploidy

The ploidy of the species being analyzed

is.reference

The dosage calls value is based on the count of reference alleles (TRUE/FALSE)

Examples

# example code

# example numeric genotype matrix for a tetraploid
n_ind <- 5
n_snps <- 10

geno <- matrix(as.numeric(sample(0:4, n_ind * n_snps, replace = TRUE)), nrow = n_snps, ncol = n_ind)
colnames(geno) <- paste0("Ind", 1:n_ind)
rownames(geno) <- paste0("SNP", 1:n_snps)
ploidy <- 4

# Output matrix with the allele count reversed
results <- flip_dosage(geno, ploidy, is.reference = TRUE)

print(results)