anal.multi | R Documentation |
Run multiple simulations of a backcross, analyzed using ANOVA, CIM and forward selection (with both BIC and permutation tests).
anal.multi(n.sim=1000, cim.steps=c(3,5,7,9,11), bic.mult=c(2,2.5,3),
max.steps=13, n.perm=1000, alpha=0.05, thresh=NULL, drop=1.5,
n.ind=100, n.mar=rep(11,9), mar.sp=rep(10,10*9),
qtl.chr=c(1,1,2,2,3,4,5), qtl.mar=c(4,8,4,8,6,4,1),
qtl.dist=rep(0,7), qtl.eff=c(1,1,1,-1,1,1,1)/2,
sigma=1)
n.sim |
Number of simulation replicates. |
cim.steps |
Number of steps in forward selection prior to CIM analysis. |
bic.mult |
Multipliers for BIC. |
max.steps |
Maximum number of steps in forward selection. |
n.perm |
Number of permutation replicates in permutation tests. |
alpha |
Significance level in permutation tests. |
thresh |
LOD thresholds for ANOVA and CIM. Should be length 1 or 1+length(cim.steps). If NULL and the chromosome structure and number of individuals match simulations that I've already done, we use my estimated LOD thresholds. |
drop |
Drop in LOD that is required between inferred QTLs. Should be length 1 or 1+length(cim.steps). |
n.ind |
Number of backcross individuals. |
n.mar |
Vector indicating the number of markers on each chromosome. |
mar.sp |
Vector of length sum(n.mar)-n.chr-1, giving the inter-marker spacings in cM. |
qtl.chr |
Chromosomes on which qtls are sitting. |
qtl.mar |
Markers to the left of each qtl, numbered 1, 2, ... |
qtl.dist |
Distance between qtl and marker to left, in cM. |
qtl.eff |
QTL effects. |
sigma |
Residual (environmental) standard deviation. |
A list of length 2+n.cim+n.bic, whose components correspond to the results of ANOVA, CIM, forward selection with BIC, and forward selection with permutation tests. Each component of this list is itself a list of length n.sim, with each component giving the chromosome numbers and marker numbers of the identified QTLs.
Karl W Broman, broman@wisc.edu
Broman, K. W. (1997) Identifying quantitative trait loci in experimental crosses. PhD dissertation, Department of Statistics, University of California, Berkeley.
simbc
, sim.null
,
sim.mcmc
, anal.multi2
## Not run: results <- anal.multi(n.sim=10)
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