To multiple QTL analysis

[Othmane Lamoumni]

Hello everyone,

I would just like your help for confirming some of my conclusions:

1- (IM) as a single-QTL model is conducted using scanone() on after running sim_geno() and calc_genoprob():

cross <- read.cross(cross_file)

cross_sim <- sim_geno(cross)

cross_gen <-calc.genoprob(cross_sim)

IM_scan <- scanone(cross_gen)

IM_scan_perm <- scanone(cross_gen, n.perm = n) #To define threshold

2- Then, in order to conduct a multi-QTL analysis, there are three possible ways (I'm not familiar yet with Bayesian method, so)

- CIM: using cim() function (with or without a prior simulation??)

- MQM: which possesses its own pipeline as I understood

- Perform Two-QTL analysis: scantwo(), use the results to built a model with a formula, and a qtl object: makeqtl(), then use the two objects for fitqtl() and/or? stepwiseqtl().

           scantwo(cross_gen)

           my_form <-  y ~ Q1 + Q2 + Q3....

           my_qtl <- makeqtl(cross_gen, c(chromosomes), c(positions))

           fitqtl(cross_gen, qtl, my_form, get.ests=T) / stepwiseqtl(cross_gen, qtl, my_form)

I hope my message is clear, I have other detailed questions, but I would like to have a clear global picture first.

Thank you and I appreciate your help 

Othmane