R: Tests for parent-child annotation enchrichment in lineage...

testEdges {alakazam} | R Documentation

## Tests for parent-child annotation enchrichment in lineage trees

### Description

`testEdges` performs a permutation test on a set of lineage trees to determine the significance of an annotation's association with parent-child relationships.

### Usage

    testEdges(graphs, field, indirect = FALSE, exclude = c("Germline", NA),
      nperm = 200, progress = FALSE)

### Arguments

`graphs` | list of igraph objects with vertex annotations.
`field` | string defining the annotation field to permute.
`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 permutation.
`nperm` | number of permutations to perform.
`progress` | if `TRUE` show a progress bar.

### Value

An EdgeTest object containing the test results and permutation realizations.

### See Also

Uses tableEdges and permuteLabels. See plotEdgeTest for plotting the permutation distributions.

### Examples

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

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

[Package alakazam version 0.3.0 Index]