Jacquard ordering

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Description

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

Usage

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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?

Details

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

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.

Author(s)

Fiona Grimson

Examples

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## 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 )