qdg.perm.test {qtlnet} | R Documentation |
Conduct permutation test for LOD score of edge direction on directed graph
Description
Conduct permutation test for LOD score of edge direction on directed graph.
Usage
qdg.perm.test(cross, nperm, node1, node2, common.cov = NULL,
DG, QTLs, addcov = NULL, intcov = NULL)
## S3 method for class 'qdg.perm.test'
summary(object, ...)
## S3 method for class 'qdg.perm.test'
print(x, ...)
Arguments
cross |
Object of class |
nperm |
Number of permutations. |
node1 |
Character string with name of a phenotype nodes. |
node2 |
Character string with name of a phenotype nodes. |
common.cov |
Character string with name of common phenotype covariates. |
DG |
Directed graph of class |
QTLs |
List of objects of class |
addcov |
Names of additive covariates. Must be valid phenotype
names in |
intcov |
Names of additive covariates. Must be valid phenotype
names in |
x , object |
Object of class |
... |
Additional arguments ignored. |
Details
qdg.perm.test
performs nperm
permutation-based test
of LOD score for an
edge of a directed graph.
Value
List composed by:
pvalue |
Permutation p-value. |
obs.lod |
Observed LOD score. |
PermSample |
Permutation LOD scores sample. |
node1 |
Character string with name of a phenotype nodes. |
node2 |
Character string with name of a phenotype nodes. |
References
Chaibub Neto et al. (2008) Inferring causal phenotype networks from segregating populations. Genetics 179: 1089-1100.
Examples
data(glxnet)
glxnet.cross <- calc.genoprob(glxnet.cross)
set.seed(1234)
glxnet.cross <- sim.geno(glxnet.cross)
## Should really use nperm = 1000 here.
qdg.perm.test(glxnet.cross, nperm = 10, "Glx", "Slc1a2",
DG = glxnet.qdg$DG, QTLs = glxnet.qtl)