testEdges - Tests for parent-child annotation enchrichment in lineage trees
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 )
- list of igraph objects with vertex annotations.
- string defining the annotation field to permute.
FALSEcount direct connections (edges) only. If
TRUEwalk through any nodes with annotations specified in the
argumentto count indirect connections. Specifying
exclude=NULLwill have no effect.
- vector of strings defining
fieldvalues to exclude from permutation.
- number of permutations to perform.
TRUEshow a progress bar.
An EdgeTest object containing the test results and permutation realizations.
# Define example tree set graphs <- ExampleTrees[1-10] # Perform edge test on isotypes x <- testEdges(graphs, "c_call", nperm=10)
Error in ecdf(d): ‘x’ must have 1 or more non-missing values
Error in h(simpleError(msg, call)): error in evaluating the argument ‘x’ in selecting a method for function ‘print’: object ‘x’ not found