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. 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, "c_call", nperm=10)
print(x)

      parent     child count   expected    pvalue
1       IGHA      IGHA    39  60.400000 0.9000000
2       IGHA IGHA,IGHG     3   3.200000 0.5000000
3       IGHA      IGHG     2   4.400000 0.9000000
4  IGHA,IGHG      IGHA    29  10.166667 0.0000000
5  IGHA,IGHG IGHA,IGHG     1   1.333333 0.3333333
6  IGHA,IGHG      IGHG    24   4.600000 0.0000000
7  IGHD,IGHG      IGHG     8   1.125000 0.0000000
8       IGHG      IGHA     1   4.200000 1.0000000
9       IGHG IGHD,IGHG     1   1.000000 0.0000000
10      IGHG      IGHG   112 135.700000 1.0000000

See also¶

Uses tableEdges and permuteLabels. See plotEdgeTest for plotting the permutation distributions.