qdg.perm.test {qdg}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 cross (see read.cross).
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 QDG
QTLs List of objects of class qtl.
addcov Names of additive covariates. Must be valid phenotype names in cross. Expanded to include all intcov names.
intcov Names of additive covariates. Must be valid phenotype names in cross.
x,object Object of class qdg.perm.test.
... 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

## Not run: 
example(glxnet)
## End(Not run)

[Package qdg version 1.0.0 Index]