R: Tests for MRCA annotation enrichment in lineage trees

testMRCA {alakazam} | R Documentation

## 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.

### See Also

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

### Examples

    # Define example tree set
    graphs <- ExampleTrees[1-10]

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

[Package alakazam version 0.3.0 Index]