R: Tabulate the number of edges between annotations within a...

tableEdges {alakazam} | R Documentation

## Tabulate the number of edges between annotations within a lineage tree

### Description

`tableEdges` creates a table of the total number of connections (edges) for each unique pair of annotations within a tree over all nodes.

### Usage

    tableEdges(graph, field, indirect = FALSE, exclude = NULL)

### Arguments

`graph` | igraph object containing an annotated lineage tree.
`field` | string defining the annotation field to count.
`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 counts. Edges that either start or end with the specified annotations will not be counted. If `NULL` count all edges.

### Value

A data.frame defining total annotation connections in the tree with columns:

- `PARENT`: parent annotation

- `CHILD`: child annotation

- `COUNT`: count of edges for the parent-child relationship

### See Also

See testEdges for performed a permutation test on edge relationships.

### Examples

    # Define example graph
    graph <- ExampleTrees[[23]]

    # Count direct edges between isotypes including inferred nodes
    tableEdges(graph, "ISOTYPE")

    # Count direct edges excluding edges to and from germline and inferred nodes
    tableEdges(graph, "ISOTYPE", exclude=c("Germline", NA))

    # Count indirect edges walking through germline and inferred nodes
    tableEdges(graph, "ISOTYPE", indirect=TRUE, exclude=c("Germline", NA))

[Package alakazam version 0.3.0 Index]