annotation {simer}

Annotation simulation

Description

Generating a map with annotation information

Usage

annotation(SP, verbose = TRUE)

Arguments

SP

a list of all simulation parameters.

verbose

whether to print detail.

Details

Build date: Nov 14, 2018 Last update: Jul 10, 2022

Value

the function returns a list containing

$map$pop.map

the map data with annotation information.

$map$species

the species of genetic map, which can be "arabidopsis", "cattle", "chicken", "dog", "horse", "human", "maize", "mice", "pig", and "rice".

$map$pop.marker

the number of markers.

$map$num.chr

the number of chromosomes.

$map$len.chr

the length of chromosomes.

$map$qtn.model

the genetic model of QTN such as 'A + D'.

$map$qtn.index

the QTN index for each trait.

$map$qtn.num

the QTN number for (each group in) each trait.

$map$qtn.dist

the QTN distribution containing 'norm', 'geom', 'gamma' or 'beta'.

$map$qtn.var

the variances for normal distribution.

$map$qtn.prob

the probability of success for geometric distribution.

$map$qtn.shape

the shape parameter for gamma distribution.

$map$qtn.scale

the scale parameter for gamma distribution.

$map$qtn.shape1

the shape1 parameter for beta distribution.

$map$qtn.shape2

the shape2 parameter for beta distribution.

$map$qtn.ncp

the ncp parameter for beta distribution.

$map$qtn.spot

the QTN distribution probability in each block.

$map$len.block

the block length.

$map$maf

the maf threshold, markers less than this threshold will be exclude.

$map$recom.spot

whether to generate recombination events.

$map$range.hot

the recombination times range in the hot spot.

$map$range.cold

the recombination times range in the cold spot.

Author(s)

Dong Yin

Examples

# Generate annotation simulation parameters
SP <- param.annot(qtn.num = list(tr1 = 10))

# Run annotation simulation
SP <- annotation(SP)