customMap: Custom recombination map

In ibdsim2: Simulation of Chromosomal Regions Shared by Family Members

Custom recombination map

Description

Create custom recombination maps for use in ibdsim().

Usage

customMap(x)

Arguments

x	A data frame or matrix. See details for format specifications.

Details

The column names of x must include either

• chrom, mb and cm (sex-averaged map)

or

• chrom, mb, male and female (sex-specific map)

Upper-case letters are allowed in these names. The mb column should contain physical positions in megabases, while cm, male, female give the corresponding genetic position in centiMorgans.

Value

An object of class genomeMap.

See Also

uniformMap(), loadMap()

Examples

# A map including two chromosomes.
df1 = data.frame(chrom = c(1, 1, 2, 2),
                 mb = c(0, 2, 0, 5),
                 cm = c(0, 3, 0, 6))
map1 = customMap(df1)
map1

# Use columns "male" and "female" to make sex specific maps
df2 = data.frame(chrom = c(1, 1, 2, 2),
                 mb = c(0, 2, 0, 5),
                 male = c(0, 3, 0, 6),
                 female = c(0, 4, 0, 7))
map2 = customMap(df2)
map2

ibdsim2 documentation built on Aug. 17, 2023, 5:17 p.m.