run.do.single: run simulations for DO type experiments
In jianan/qtlintv: QTL interval estimation

Description Usage Arguments

For a fix set of parameters, generate DO pedigree and simulate crossovers, randomly generate phenotypes with main QTL and minor QTLs, then run DOQTL::scanone to do QTL mapping. save LOD score as a matrix and marker informations to result.dir.

run.do.single(method = c("sub2", "last2", "fixcc"), para, i.para, i.simu,
  i.qtlpos, output.dir = "DO.output/", result.dir = "./",
  n.simu_qtlpos = 1, n.simu = 10000, qtl.chr = 1, ochr = 2:19,
  n.mqtl = 10, n.ccgen = 15, map.whole, qtl.allpos, f.geno.chr, snps,
  design = c("nosib", "random"), selc.method = c("byfamily", "byindiv"),
  write.gp36 = FALSE, cleanup = TRUE, realpb8 = FALSE, noK = FALSE)

`method`	design method for the pedigree, choose from 'sub2' or 'last2' or 'fixcc'.
`para`	data.frame that saves all the parameter settings for the simulation
`i.para`	which setting to use for the current run
`i.simu`	which simulation is the currtent run at
`i.qtlpos`	which candidate qtlpos will be used.
`n.simu_qtlpos`	number of phenotypes for each qtl position. suggested to be 1, otherwise the result will be correlated.
`qtl.chr`	chromosome for the qtl
`ochr`	chromosomes other than qtl.chr, used to estimate kinship matrix
`n.mqtl`	number of minor qtls for the polygenic effects
`map.whole`	genetic map for all chromosomes
`qtl.allpos`	named vector of all candidate qtl positions.
`f.geno.chr`	founder genotype for QTL chromosome.
`snps`	SNP information saved in a data.frame: name, chr and position. Only for SNPs on the QTL chromosome.
`design`	'nosib' or 'random'
`write.gp36`	logic value
`cleanup`	logic value
`realpb8`	will the real 8 allele probabilities be used while mapping.
`noK`	do we control for Kinship matrix while mapping.