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.
1 2 3 4 5 6 | run.do(method = c("sub2", "last2", "fixcc"), para, i.para, i.simu,
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 |
n.simu_qtlpos |
number of phenotypes for each qtl position. suggested to be 1, otherwise the result will be correlated. |
n.simu |
total number of simulations needed. |
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' |
selc.method |
Method used to select the individuals from last generation in DO pedigree. |
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. |
i.qtlpos |
which candidate qtlpos will be used. |
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