hypredSNPdist: Find the genetic distance and recombination frequency between...
In timflutre/hypred: Simulation of Genomic Data in Applied Genetics

Description Usage Arguments Details Value See Also Examples

A generic function to find the genetic distance and recombination frequency between two SNP on a chromosome.

hypredSNPdist(object, ...)
## S4 method for signature 'hypredGenome'
hypredSNPdist(object, chromosome, SNP1, SNP2,
block = FALSE)

`object`	an object of a class that holds information on map positions of loci, typically an `"hypredGenome"` object.
`chromosome`	The chromosome on which the SNP are, given as integer.
`SNP1`	The first SNP, given as integer.
`SNP2`	The second SNP, given as integer. This SNP must have a higher index than `SNP1`.
`block`	logical argument indicating if the map positions of the SNP themselfes should be used (`FALSE`) or the map positions of the block in which they are located (`TRUE`).
`...`	Methods may require further arguments.

The recombination frequency is calculated by the inverse of the Haldane mapping function.

A two row, one column matrix with the genetic distance (in M) in row one and the recombination frequency in row two.

The function hypredDInv which is used by the hypredGenome method.

## one chromosome of length 1 M and 5 SNP

map <- hypredGenome(1, 1.0, 5)

## distance and recombination frequency between SNP 1 and 3 on
## chromosome 1
hypredSNPdist(map,1,1,3)