testMRCA - 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, "c_call", nperm=10)

print(x)

  annotation count  expected    pvalue
1       IGHA    16 13.300000 0.0000000
2  IGHA,IGHG     1  1.142857 0.1428571
3       IGHG    31 33.700000 0.9000000

See also¶

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