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Get SNP or InDel alleles and possible genotypes from genotype calls in KASP data.

Source: R/kasp_validation.R
get_alleles.Rd

Get SNP or InDel alleles and possible genotypes from genotype calls in KASP data.

Usage

get_alleles(x, sep = ":", data_type = c("kasp", "agriplex"))

Arguments

x

A character vector of KASP genotype calls in one reaction plate.

sep

A character used as separator for genotype calls, default is a colon.

data_type

A character value indicating the data source; either `kasp` or `agriplex`.

Value

A list object with `length = 2` consisting of marker alleles and possible genotypes in x.

Examples

# example code
# \donttest{
# Simulate a typical KASP genotype call
set.seed(123)
x <- sample(c("A:A", "A:-", "-:-", "Uncallable", "?"),
            size = 96,
            replace = TRUE)

# Assign NTC wells
x[c(88, 96)] <- 'NTC'

# Get alleles and expected genotypes
alleles <- get_alleles(x = x, data_type = 'kasp')
# }