ibdsim2 (version 1.2)

customMap: 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.

Value

An object of class genomeMap.

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.

See Also

uniformMap(), loadMap()

Examples

# NOT RUN {
# 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

# }