R: Tests for MRCA annotation enrichment in lineage trees

testMRCA {alakazam}

R Documentation

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.

Examples


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

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