run.do.fixcc: run simulations for DO type experiments, with the same pre-CC...
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.fixcc(para, i.para, j.simu, output.dir = "DO.output/",
  result.dir = "./", n.simu = 1, qtl.chr = 1, ochr = 2:19,
  n.mqtl = 10, map.whole, qtl.allpos, f.geno.chr, snps, design = c("nosib",
  "random"), write.gp36 = FALSE, cleanup = TRUE)

`para`	data.frame that saves all the parameter settings for the simulation
`i.para`	which setting to use for the current run
`j.simu`	which simulation is the currtent run at
`n.simu`	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