loadMap {ibdsim2}

Load a built-in genetic map

Description

This function loads one of the built-in genetic maps. Currently, the only option is a detailed human recombination map, based on the publication by Halldorsson et al. (2019).

Usage

loadMap(map = "decode19", chrom = 1:22, uniform = FALSE, sexAverage = FALSE)

Arguments

map

The name of the wanted map, possibly abbreviated. Currently, the only valid choice is "decode19" (default).

chrom

A vector containing a subset of the numbers 1,2,...,23, indicating which chromosomes to load. As a special case, chrom = "X" is synonymous to chrom = 23. Default: 1:22 (the autosomes).

uniform

A logical. If FALSE (default), the complete inhomogeneous map is used. If TRUE, a uniform version of the same map is produced, i.e., with the correct physical range and genetic lengths, but with constant recombination rates along each chromosome.

sexAverage

A logical, by default FALSE. If TRUE, a sex-averaged map is returned, with equal recombination rates for males and females.

Details

For reasons of speed and efficiency, the map published by map Halldorsson et al. (2019) has been thinned down to around 60 000 data points.

By setting uniform = TRUE, a uniform version of the map is returned, in which each chromosome has the same genetic lengths as in the original, but with constant recombination rates. This gives much faster simulations and may be preferable in some applications.

Value

An object of class genomeMap, which is a list of chromMap objects. A chromMap is a list of two matrices, named "male" and "female", with various attributes:

• physStart: The first physical position (Mb) on the chromosome covered by the map

• physEnd: The last physical position (Mb) on the chromosome covered by the map

• physRange: The physical map length (Mb), equal to physEnd - physStart

• mapLen: A vector of length 2, containing the centiMorgan lengths of the male and female strands

• chrom: A chromosome label

• Xchrom: A logical. This is checked by ibdsim() and other function, to select mode of inheritance

References

Halldorsson et al. Characterizing mutagenic effects of recombination through a sequence-level genetic map. Science 363, no. 6425 (2019).

See Also

uniformMap(), customMap()

Examples

# By default, the complete map of all 22 autosomes is returned
loadMap()

# Uniform version
m = loadMap(uniform = TRUE)
m

# Check chromosome 1
m1 = m[[1]]
m1
m1$male
m1$female

# The X chromosome
loadMap(chrom = "X")[[1]]