alakazam (version 1.1.0)

testEdges: Tests for parent-child annotation enchrichment 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

# NOT RUN {
# Define example tree set
graphs <- ExampleTrees[1-10]

# Perform edge test on isotypes
x <- testEdges(graphs, "c_call", nperm=10)
print(x)
# }
# NOT RUN {
# }