testMRCA - Tests for MRCA annotation enrichment in lineage trees
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
testMRCA( graphs, field, root = "Germline", exclude = c("Germline", NA), nperm = 200, progress = FALSE )
- list of igraph object containing annotated lineage trees.
- string defining the annotation field to test.
- name of the root (germline) node.
- vector of strings defining
fieldvalues to exclude from the set of potential founder annotations.
- number of permutations to perform.
TRUEshow a progress bar.
An MRCATest object containing the test results and permutation realizations.
# Define example tree set graphs <- ExampleTrees[1-10] # Perform MRCA test on isotypes x <- testMRCA(graphs, "c_call", nperm=10)
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