testEdges: Tests for parent-child annotation enrichment in lineage trees
Description
testEdges performs a permutation test on a set of lineage trees to determine
the significance of an annotation's association with parent-child relationships.
An EdgeTest object containing the test results and permutation
realizations.
Arguments
graphs
list of igraph objects with vertex annotations.
field
string defining the annotation field to permute.
indirect
if FALSE count direct connections (edges) only. If
TRUE walk through any nodes with annotations specified in
the argument to count indirect connections. Specifying
indirect=TRUE with exclude=NULL will have no effect.
exclude
vector of strings defining field values to exclude from
permutation.
nperm
number of permutations to perform.
progress
if TRUE show a progress bar.
See Also
Uses tableEdges and permuteLabels.
See plotEdgeTest for plotting the permutation distributions.