run.ail: run simulations for AIL

In jianan/qtlintv: QTL interval estimation

Description

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

Usage

run.ail(method = c("sub2", "last2"), para, i.para, n.simu,
  result.dir = "./", qtl.chr = 1, ochr = 2:19, n.mqtl = 10,
  design = c("nosib", "random"), eq.spacing = TRUE, gap.middle = 50,
  step = 0.1, n.mar.cM = 2)

Arguments

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
n.simu	number of phenotypes for the current run
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
design	'nosib' or 'random'

jianan/qtlintv documentation built on May 19, 2019, 9:29 a.m.