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 |

`nperm` |
number of permutations to perform. |

`progress` |
if |

### 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, "c_call", nperm=10)
print(x)
```

[Package

*alakazam*version 1.3.0 Index]