allJaq: Jacquard ordering

In IBDLabels: Convert Between Different IBD-State Labelling Schemes.

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?

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

## 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 )

IBDLabels documentation built on May 2, 2019, 5:56 p.m.