progeny {QTLEMM}

Progeny Simulation

Description

Generate simulated phenotype and genotype data for a specified generation from various breeding schemes.

Usage

progeny(
  QTL,
  marker,
  type = "RI",
  ng = 2,
  cM = TRUE,
  E.vector = NULL,
  h2 = 0.5,
  size = 200
)

Arguments

QTL

matrix. A q*2 matrix contains the QTL information, where the row dimension 'q' represents the number of QTLs in the chromosomes. The first column labels the chromosomes where the QTLs are located, and the second column labels the positions of QTLs (in morgan (M) or centimorgan (cM)).

marker

matrix. A k*2 matrix contains the marker information, where the row dimension 'k' represents the number of markers in the chromosomes. The first column labels the chromosomes where the markers are located, and the second column labels the positions of markers (in morgan (M) or centimorgan (cM)). It's important to note that chromosomes and positions must be sorted in order.

type

character. The population type of the dataset. Includes backcross (type="BC"), advanced intercross population (type="AI"), and recombinant inbred population (type="RI"). The default value is "RI".

ng

integer. The generation number of the population type. For instance, in a BC1 population where type="BC", ng=1; in an AI F3 population where type="AI", ng=3.

cM

logical. Specify the unit of marker position. If cM=TRUE, it denotes centimorgan; if cM=FALSE, it denotes morgan.

E.vector

vector. Set the effect of QTLs. It should be a named vector, where the names of elements represent the effects of QTLs and their interactions. For example: the additive effect of QTL1 is coded as "a1"; the dominant effect of QTL2 is coded as "d2"; the interaction of the additive effect of QTL2 and the dominant effect of QTL1 is coded as "a2:d1". So, if the additive effect of QTL1 is 2, the dominant effect of QTL2 is 5, and the interaction of the additive effect of QTL2 and the dominant effect of QTL1 is 3, the user should input: E.vector = c("a1"=2, "d2"=5, "a2:d1"=3). If E.vector=NULL, the phenotypic value will not be simulated.

h2

numeric. Set the heritability for simulated phenotypes. It should be a number between 0 and 1.

size

numeric. The population size of simulated progeny.

Value

phe

The phenotypic value of each simulated progeny.

E.vector

The effect vector used in this simulation.

marker.prog

The marker genotype of each simulated progeny.

QTL.prog

The QTL genotype of each simulated progeny.

VG

The genetic variance of this population.

VE

The environmental variance of this population.

genetic.value

The genetic value of each simulated progeny.

References

Haldane J.B.S. 1919. The combination of linkage values and the calculation of distance between the loci for linked factors. Genetics 8: 299–309.

Examples

# load the example data
load(system.file("extdata", "exampledata.RDATA", package = "QTLEMM"))

# run and result
result <- progeny(QTL, marker, type = "RI", ng = 5, E.vector = c("a1" = 2, "d2" = 5, "a2:d1" = 3),
h2 = 0.5, size = 200)
result$phe