Description Usage Arguments Details Value Examples
Significance Threshold of Genome Scan
1 2 3 4 |
geno |
genotype probabilities (" |
pheno |
data frame with phenotypes |
pheno.cols |
selection of phenotype's column(s) |
covar |
(additive) covariates |
procedure |
procedure to do the inference, see Details |
G |
genetic similarity matrix or a list of genetic similarity matrices or |
n.perm |
number of permutations |
alpha |
level of significance |
subjects |
subseting of subjects |
markers |
subseting of markers |
keep.lods |
if TRUE maximum lod values thate have been used for threshold calculation are returned as attribute 'maxlods' |
... |
parameters passed to |
Currently, three procedures are implemented: linear model (LM), linear mixed model (LMM) and linear mixed model - leave one chromosome out (LOCO).
numeric
1 2 3 4 5 6 7 | data(fake.f2, package="qtl")
fake.f2 <- calc.genoprob(fake.f2)
# warning, n.perm=10 is too low for practical purposes (but fast)
scan1.threshold(fake.f2, procedure="LM", n.perm=10)
scan1.threshold(fake.f2, procedure="LMM", n.perm=10)
scan1.threshold(fake.f2, procedure="LOCO", n.perm=10)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.