R: Tests for parent-child annotation enchrichment in lineage...

testEdges {alakazam}

R Documentation

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. If `TRUE` walk through any nodes with annotations specified in the `argument` to count indirect connections. Specifying `indirect=TRUE` with `exclude=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, "ISOTYPE", nperm=10)
print(x)