testEdges - Tests for parent-child annotation enchrichment in lineage trees
Description¶
testEdges
performs a permutation test on a set of lineage trees to determine
the significance of an annotation’s association with parent-child relationships.
Usage¶
testEdges(
graphs,
field,
indirect = FALSE,
exclude = c("Germline", NA),
nperm = 200,
progress = FALSE
)
Arguments¶
- graphs
- list of igraph objects with vertex annotations.
- field
- string defining the annotation field to permute.
- indirect
- if
FALSE
count direct connections (edges) only. IfTRUE
walk through any nodes with annotations specified in theargument
to count indirect connections. Specifyingindirect=TRUE
withexclude=NULL
will have no effect. - exclude
- vector of strings defining
field
values to exclude from permutation. - nperm
- number of permutations to perform.
- progress
- if
TRUE
show a progress bar.
Value¶
An EdgeTest object containing the test results and permutation realizations.
Examples¶
# 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
print(x)
Error in h(simpleError(msg, call)): error in evaluating the argument ‘x’ in selecting a method for function ‘print’: object ‘x’ not found
See also¶
Uses tableEdges and permuteLabels. See plotEdgeTest for plotting the permutation distributions.