Specimen: Class providing object with methods to mimic in silico...

In isqg: In Silico Quantitative Genetics

Class providing object with methods to mimic in silico Specimens

Description

Mean to mimic a in silico Specimens. It is the working instances of the simulator.

Details

Object of R6 class that points to C++ objetcs.

Value

Objects of R6 class with methods to mimic in silico Specimens.

Public fields

.ptr

External pointer to the instance of the C++ class Specie.

Methods

Public methods

• .R_Specimen_ctor$new()

• .R_Specimen_ctor$print()

• .R_Specimen_ctor$alpha()

• .R_Specimen_ctor$genotype()

• .R_Specimen_ctor$cross()

• .R_Specimen_ctor$selfcross()

• .R_Specimen_ctor$dh()

• .R_Specimen_ctor$mirror()

• .R_Specimen_ctor$look()

• .R_Specimen_ctor$clone()

---

Method new()

Create an instance of a Specimen.

Usage

.R_Specimen_ctor$new(ptr)

Arguments

ptr

an Smart pointer to an instance of a Specimen C++ class.

Returns

A new 'Specimen' object.

---

Method print()

Print/Show an instance of the Specimen class.

Usage

.R_Specimen_ctor$print(...)

Arguments

...

further arguments to be passed to print.

---

Method alpha()

Evaluates the breeding value.

Usage

.R_Specimen_ctor$alpha(trait)

Arguments

trait

an instance of the class Trait.

Returns

the breeding value of the specimen for the given trait.

---

Method genotype()

Codify Specimen's Genotypes.

Usage

.R_Specimen_ctor$genotype(phase = FALSE)

Arguments

phase

logical should the codes keep the phase.

Returns

A numeric or character vector with the codified Specimen's genotypes.

---

Method cross()

Performs the simple bi-parental cross.

Usage

.R_Specimen_ctor$cross(n = 1, gid)

Arguments

n

a length-one integer vector with the size of the progeny.

gid

instance of the class specimen which will be used to mate.

Returns

a size n list with instances of the class Specimen that represent new individuals belonging to the progeny of the respective mating scheme.

---

Method selfcross()

Performs the selfcross.

Usage

.R_Specimen_ctor$selfcross(n = 1, replace = FALSE)

Arguments

n

a length-one integer vector with the size of the progeny.

replace

logical scalar indicating if the outcome of the function will replace the current instance of the Specimen

Returns

a size n list with instances of the class Specimen that represent new individuals belonging to the progeny of the respective mating scheme.

---

Method dh()

Performs the double-haploid duplication

Usage

.R_Specimen_ctor$dh(n = 1, replace = FALSE)

Arguments

n

a length-one integer vector with the size of the progeny.

replace

logical scalar indicating if the outcome of the function will replace the current instance of the Specimen

Returns

a size n list with instances of the class Specimen that represent new individuals belonging to the progeny of the respective mating scheme.

---

Method mirror()

Generates a 'mirrored' specimen.

Usage

.R_Specimen_ctor$mirror()

Returns

an instance of the Specimen class with all loci mirrored.

---

Method look()

Acess specific locus' value from specimen.

Usage

.R_Specimen_ctor$look(snp, phase = FALSE)

Arguments

snp

an character string with the name of the locus to lookup.

phase

logical should the codes keep the phase.

Returns

the genotype of the given locus.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

.R_Specimen_ctor$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

isqg documentation built on Oct. 18, 2022, 9:07 a.m.