sim.autoMarkers {polySegratio}R Documentation

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 overide 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 porportions, list with components
    ratio
    segregation proportions,
    ploidy.level
    level of ploidy 4,6,8, ...
    ploidy.name
    tetraploid, ... , 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.dosages
    summary of no.s in each dosage
    names
    names 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 distrubution employed to generate Binomial probabilities
call matches arguments when function called

Note

For use in simulation studies, other parameters such as the true dosage of each marker are also returned. Also, if extra binomial variation or overdispersion is requested then a beta-binomial distribution is employed to simulate marker data.Note that as the 'shape1' parameter becomes larger, the resulting marker data are less overdispersed.

Author(s)

Peter Baker p.baker1@uq.edu.au

See Also

simAutoMarkers, print.simAutoMarkers, plot.simAutoMarkers, segRatio

Examples


## 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="homo",n.markers=20,n.individuals=10)
print(a2)


[Package polySegratio version 0.2-3 Index]