testMRCA: Tests for MRCA annotation enrichment in lineage trees

In alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis

Tests for MRCA annotation enrichment in lineage trees

Description

testMRCA performs a permutation test on a set of lineage trees to determine the significance of an annotation's association with the MRCA position of the lineage trees.

Usage

testMRCA(
  graphs,
  field,
  root = "Germline",
  exclude = c("Germline", NA),
  nperm = 200,
  progress = FALSE
)

Arguments

graphs	list of igraph object containing annotated lineage trees.
field	string defining the annotation field to test.
root	name of the root (germline) node.
exclude	vector of strings defining field values to exclude from the set of potential founder annotations.
nperm	number of permutations to perform.
progress	if TRUE show a progress bar.

Value

An MRCATest object containing the test results and permutation realizations.

See Also

Uses getMRCA and getPathLengths. See plotMRCATest for plotting the permutation distributions.

Examples

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

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

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