sim.sigthr: Simulate a significance threshold for (composite) interval mapping
Description
Generate a significance threshold by simulating from the
null hypothesis. Phenotypic values for the observed
genetic data are simulated to represent data with no QTL,
and a genomewide p-value threshold is calculated.
Usage
sim.sigthr(mpcross, nsim = 100, alpha = 0.05, pindex = 1, step = 0, ncov = 0, ...)
Arguments
mpcross
Object of class mpcross
nsim
Number of null datasets to simulate; default
is 100
alpha
Significance threshold for QTL p-values
pindex
Index of phenotype (if more than one in
dataset)
step
Step size at which to compute the QTL
profile. Default is 0, at midpoints of marker intervals
ncov
Number of marker covariates to search for -
default is 0 for interval mapping
Value
List with components: - alpha
- Input significance
threshold
- nsim
- Input number of simulated
datasets
- minp
- Genomewide minimum p-value for each
simulated dataset
- thr
- Empirical p-value
threshold