sim.autoCross {polySegratio}

Simulate dominant markers for an autopolyploid cross for all parental types

Description

Simulates dominant markers from an autopolyploid cross given the ploidy level and/or expected segregation ratios and the proportions in each dosage marker class. This is a wrapper to sim.autoMarkers to generate markers for ‘10’, ‘01’ and ‘11’ parents

Usage

sim.autoCross(ploidy.level, prop.par.type = structure(c(0.4, 0.4, 0.2),
names = c("p10", "p01", "p11")), n.markers = 500, n.individuals = 200,
dose.proportion, true.seg.ratios, no.dosage.classes,
marker.names = paste("M", 1:n.markers, sep = "."),
individual.names = paste("X", 1:n.individuals, sep = "."),
parent.names = c("P.1", "P.2"), seed)

Arguments

ploidy.level

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

prop.par.type

the proportion of markers generated from each parental type '10', '01' and '11'. Note that the exact number will be randomly generated from the multinomial distribution (Default: c(0.4,0.4,0.2))

n.markers

number of markers (Default: 500)

n.individuals

number of individuals in the cross (Default: 200)

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 NB: If a vector is supplied the dose.proportion is same for each parental type otherwise as list with components ‘p01’, ‘p10’ and ‘p11’

true.seg.ratios

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

no.dosage.classes

numeric vector containing the number of dosage classes

marker.names

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

individual.names

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

parent.names

numeric vector of length 2 containing columns of marker matrix containing parental markers (Default: first 2 columns)

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 simAutoCross containing

markers

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

true.dosage

true doses for each marker

name.true.dose

names of true doses for each marker

p10

object of class simAutoMarkers for parental type ‘10’

p01

object of class simAutoMarkers for parental type ‘01’

p11

object of class simAutoMarkers for parental type ‘11’

ploidy.level

the number of homologous chromosomes as numeric (single value)

prop.par.type

proportion of markers for each parental type ‘p01’, ‘p10’ and ‘p11’

n.markers

number of markers (Default: 500)

n.individuals

number of individuals in the cross (Default: 200)

dose.proportion

proportion in each dose – if numeric vector is the same for ‘p01’, ‘p10’ and ‘p11’ else a list with components ‘p01’, ‘p10’ and ‘p11’

no.dosage.classes

number in each dosage class

no.parType

number in each parental type

time.generated

time/date when data set generated

seed

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

call

matches arguments when function called

Note

All parameters except the proportions of marker dosage types can be left at the default. If only one value is set, then individual list components will be assumed to be equal. The marker matrix is prepended with parental marker alleles. An alternative is to simply create each group using sim.automarkers and cbind them.

Author(s)

Peter Baker [e-mail]

See Also

simAutoCross,simAutoMarkers, sim.autoMarkers

Examples

p1 <- sim.autoCross(4, dose.proportion=c(0.7,0.3), n.markers=20, n.indiv=10)
print(p1)

p2 <- sim.autoCross(4, dose.proportion=list(p01=c(0.7,0.3),p10=c(0.7,0.3),p11=c(0.6,0.2,0.2)))
print(p2)