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)