sim.autoCross: Simulate dominant markers for an autopolyploid cross for all...

In polySegratio: Simulate and Test Marker Dosage for Dominant Markers in Autopolyploids

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)

polySegratio documentation built on May 2, 2019, 7:26 a.m.