allVec: IBD state vectors

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

Description

These vectors are complete descriptions of the IBD state. There is one vector element per gamete. The first gamete is always numbered one, with subsequent gametes being given the same number if they are IBD with a previous gamete, or a new number if they are not.

For example in (1,2,2,3), the second and third gametes are IBD.

Note that label starts at ZERO. When converting label to vector, if the label is invalid the returned vector has NA elements.

Usage

allVec(ngam)

vec2label(vec)

label2vec(label, ngam) 

fgl2vec(vec)

Arguments

ngam	Number of gametes if a label is supplied, otherwise number of gametes will be determined by the length of the vector.
vec	IBD state description vector. Must be a single vector.
label	IBD label. Must be an integer.

Value

For allVec, a matrix of the vectors for each label is produced, with a vector on each row and a row for each label. The labels are the row names.

For vec2label and label2vec an integer label or vector is prouduced respectively. If the input label is invalid the returned vector contains NA elements.

fgl2vec returns a vector of the same length as the input, renumbered. The vec2label function calls fgl2vec, so any vector supplied will be renumbered. If (1,1,1,3) is given, it will be renumbered (1,1,1,2) and given the label 1, not 2.

Author(s)

Fiona Grimson

Examples

## Vectors for all labels
allVec( ngam = 4 )

## Convert vector to label, with renumbering or without
vec2label( c(1,1,1,3))
vec2label( c(1,1,1,2)) 

## Convert label to vector
label2vec( 1, ngam = 4 )
label2vec( 2, ngam = 4 )
label2vec( 2, ngam = 6 ) 

## renumbering
fgl2vec( c(1,1,1,3) )
fgl2vec( c(5,1,5,6) ) 

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