testMRCA: Tests for MRCA annotation enrichment in lineage trees

Description Usage Arguments Value See Also Examples

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

1
2
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.

See Also

Uses getMRCA and getPathLengths. See plotMRCATest for plotting the permutation distributions.

Examples

1
2
3
4
5
6
# Define example tree set
graphs <- ExampleTrees[1-10]

# Perform MRCA test on isotypes
x <- testMRCA(graphs, "ISOTYPE", nperm=10)
print(x)


Search within the alakazam package
Search all R packages, documentation and source code

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.