IBDLabels (version 1.1)

allJaq: Jacquard ordering

Description

Jacquard ordering for 4-gamete IBD states. Can be phased (15 states) or unphased (9 states).

Usage

allJaq()
jaq2label(jaq, phased = TRUE )
label2jaq(label, phased = TRUE )

Arguments

jaq

Jacquard state, either phased or unphased

label

IBD label

phased

Are the jacquard states the phased (15 states) or unphased ( 9 states) versions?

Value

allJaq() produces a matrix of labels (column 1), phased-jacquard (column 2) and unphased-jacquard( column 3).label2jaq or jaq2label produces an integer converted the required index.If label is invalid an NA is returned.

Details

Note that the jacquard ordering only applies to the 4-gametes case.

Examples

## list all jacquard states
allJaq()

## Convert label to jacquard
label2jaq( 3, phased = TRUE )
label2jaq( 3, phased = FALSE )

## Convert jacquard to label
jaq2label( 9, phased = TRUE )
jaq2label( 9, phased = FALSE )