testEdges {alakazam} | R Documentation |
testEdges
performs a permutation test on a set of lineage trees to determine
the significance of an annotation's association with parent-child relationships.
testEdges(
graphs,
field,
indirect = FALSE,
exclude = c("Germline", NA),
nperm = 200,
progress = FALSE
)
graphs |
list of igraph objects with vertex annotations. |
field |
string defining the annotation field to permute. |
indirect |
if |
exclude |
vector of strings defining |
nperm |
number of permutations to perform. |
progress |
if |
An EdgeTest object containing the test results and permutation realizations.
Uses tableEdges and permuteLabels. See plotEdgeTest for plotting the permutation distributions.
# Define example tree set
graphs <- ExampleTrees[1-10]
# Perform edge test on isotypes
x <- testEdges(graphs, "c_call", nperm=10)
print(x)