addAllele {pedtools}

Add allele

Description

Extends the allele set of a marker attached to a pedigree, by adding a single allele.

Usage

addAllele(x, marker, allele, freq = 0.001, adjust = c("previous", "all"))

Arguments

x

A ped object or a list of such, or a frequency database (list of numeric vectors).

marker

The name or index of a marker attached to x.

allele

The name of the new allele.

freq

The frequency of the new allele, by default 0.001.

adjust

Either "previous" or "all", indicating how the frequencies should be adjusted so that they sum to 1. If "previous" (default), the frequencies of the original alleles are multiplied with 1 - freq. If "all", scaling is performed after adding the new allele, i.e., dividing all frequencies by 1 + freq.

Value

A copy of x with modified marker attributes.

Examples

## Ped input
x = nuclearPed() |>
  addMarker(geno = c(NA, NA, "b/c"), afreq = c(b = 0.5, c = 0.5))

y = addAllele(x, marker = 1, allele = "a")
afreq(y, 1)

z = addAllele(y, marker = 1, allele = "d", freq = 0.1, adjust = "all")
afreq(z, 1)


## Database input
db = list(M1 = c(a = .2, b = .3, c = .5),
          M2 = c("7" = .9, "8.3" = .1))
addAllele(db, marker = "M2", allele = "8")