polySegratio (version 0.2-5)

sim.autoMarkers: Simulates dominant markers from an autopolyploid cross

Description

Dominant markers are simulated from an autopolyploid cross given the ploidy level, expected segregation ratios and the proportions in each dosage marker class. This may be chosen from tetraploid to heccaidecaploid and the segregation ratios may be specified explicitly or generated automatically.

Usage

sim.autoMarkers(ploidy.level, dose.proportion, n.markers = 500,
n.individuals = 200, seg.ratios, no.dosage.classes,
type.parents = c("heterogeneous", "homozygous"),
marker.names = paste("M", 1:n.markers, sep = "."),
individual.names = paste("X", 1:n.individuals, sep = "."),
overdispersion=FALSE, shape1=50, seed)

Arguments

ploidy.level

the number of homologous chromosomes, either as numeric (single value) or as a character string containing type tetraploid, hexaploid, octoploid, …

dose.proportion

the proportion of markers to be simulated in each dosage class. Note that the exact number will be randomly generated from the multinomial distribution

n.markers

number of markers (Default: 500)

n.individuals

number of individuals in the cross (Default: 200)

seg.ratios

numeric vector containing segregation proportion to be supplied if you wish to override automatic calculations using ploidy.level

no.dosage.classes

only generate markers for the first no.dosage.classes classes (if set)

type.parents

heterogeneous for (1,0) or (0,1) homozygous for (1,1) (default: heterogeneous)

marker.names

labels for markers (Default: M.1 … M.n.markers)

individual.names

labels for offspring (Default: … X.j … )

overdispersion

logical indicating overdispersion (Default: FALSE)

shape1

shape1 parameter(s) for the beta distribution used to generate the Binomial probability p, either of length 1 or no.dosage.classes. Default: 50 which implies very little overdispersion. NB: 'shape2' is calculated from shape 1 and expected segregation ratios

seed

integer used to set seed for random number generator (RNG) which (if set) may be used to reproduce results

Value

Returns an object of class simAutoMarkers containing

markers

matrix of 0,1 dominant markers with individuals as cols and rows as markers

E.segRatio

expected segregation proportions, list with components

• ratiosegregation proportions,

• ploidy.levellevel of ploidy 4,6,8, …

• ploidy.nametetraploid, … , unknown

type.parents

heterogeneous for (1,0) or (0,1) homozygous for (1,1)

dose.proportion

proportions of markers set for each dosage class

n.markers

number of markers (Default: 500)

n.individuals

number of individuals in the cross (Default: 200)

true.doses

list containing

• dosage doses generated for each marker for simulation

• table.dosagessummary of no.s in each dosage

• namesnames for each dosage such as SD (single dose), DD (double dose), SDxSD etc

seg.ratios

object of class segRatio containing segregation ratios

time.generated

time/date when data set generated

seed

seed for random number generator seed which could be used to reproduce results (I hope)

overdispersion

either a list with components 'overdispersion': logical for whether overdispersion is set or not and if TRUE then two extra components 'shape1' and 'shape2' contain parameters for the beta distribution employed to generate Binomial probabilities

call

matches arguments when function called

See Also

simAutoMarkers, print.simAutoMarkers, plot.simAutoMarkers, segRatio

Examples

# NOT RUN {
## generate autopolyploid markers
a1 <- sim.autoMarkers(4,c(0.8,0.2),n.markers=20,n.individuals=10)
print(a1)

a2 <-
sim.autoMarkers(8,c(0.7,0.2,0.09,0.01),type.parents="homo",n.markers=20,n.individuals=10)
print(a2)

# }