testEdges: Tests for parent-child annotation enrichment in lineage trees

In alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis

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.

Usage

testEdges(
  graphs,
  field,
  indirect = FALSE,
  exclude = c("Germline", NA),
  nperm = 200,
  progress = FALSE
)

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.

Value

An EdgeTest object containing the test results and permutation realizations.

See Also

Uses tableEdges and permuteLabels. See plotEdgeTest for plotting the permutation distributions.

Examples

# Define example tree set
graphs <- ExampleTrees[1:10]

# Perform edge test on isotypes
x <- testEdges(graphs, "c_call", nperm=10)
print(x)

alakazam documentation built on Sept. 30, 2023, 9:07 a.m.