maplengths: Physical and genetic map lengths

In ibdsim2: Simulation of Chromosomal Regions Shared by Family Members

Physical and genetic map lengths

Description

Utility functions for extracting the physical or genetic length of chromosome maps and genome maps.

Usage

mapLen(x, ...)

## S3 method for class 'chromMap'
mapLen(x, sex = c("male", "female"), ...)

## S3 method for class 'genomeMap'
mapLen(x, sex = c("male", "female"), ...)

physRange(x, ...)

## S3 method for class 'chromMap'
physRange(x, ...)

## S3 method for class 'genomeMap'
physRange(x, ...)

Arguments

x	A chromMap or genomeMap object.
...	Not used.
sex	Either "male", "female" or both.

Value

mapLen() returns a numeric of the same length as sex, with the genetic length(s) in centiMorgan.

physRange() returns the physical length (in Mb) of the chromosome/genome covered by the map. For example, for a chromosome map starting at 2 Mb and ending at 8 Mb, the output is 6.

See Also

loadMap(), uniformMap()

Examples

m = loadMap(chrom = 1:2)
m

# Applied to `genomeMap` object:
physRange(m)
mapLen(m)

# Applied to `chromMap` object:
physRange(m[[1]])
mapLen(m[[1]])

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