testMRCA - Tests for MRCA annotation enrichment in lineage trees
Description¶
testMRCA
performs a permutation test on a set of lineage trees to determine
the significance of an annotation’s association with the MRCA position of the lineage
trees.
Usage¶
testMRCA(
graphs,
field,
root = "Germline",
exclude = c("Germline", NA),
nperm = 200,
progress = FALSE
)
Arguments¶
- graphs
- list of igraph object containing annotated lineage trees.
- field
- string defining the annotation field to test.
- root
- name of the root (germline) node.
- exclude
- vector of strings defining
field
values to exclude from the set of potential founder annotations. - nperm
- number of permutations to perform.
- progress
- if
TRUE
show a progress bar.
Value¶
An MRCATest object containing the test results and permutation realizations.
Examples¶
# Define example tree set
graphs <- ExampleTrees[1-10]
# Perform MRCA test on isotypes
x <- testMRCA(graphs, "c_call", nperm=10)
print(x)
annotation count expected pvalue
1 IGHA 16 13.40 0.00
2 IGHA,IGHG 1 1.75 0.75
3 IGHG 31 33.90 1.00
See also¶
Uses getMRCA and getPathLengths. See plotMRCATest for plotting the permutation distributions.