testMRCA {alakazam} | R Documentation |
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.
testMRCA( graphs, field, root = "Germline", exclude = c("Germline", NA), nperm = 200, progress = FALSE )
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 |
nperm |
number of permutations to perform. |
progress |
if |
An MRCATest object containing the test results and permutation realizations.
Uses getMRCA and getPathLengths. See plotMRCATest for plotting the permutation distributions.
# Define example tree set graphs <- ExampleTrees[1-10] # Perform MRCA test on isotypes x <- testMRCA(graphs, "c_call", nperm=10) print(x)