R: Retrieve the first non-root node of a lineage tree

getMRCA {alakazam}

R Documentation

Retrieve the first non-root node of a lineage tree

Description

getMRCA returns the set of lineage tree nodes with the minimum weighted or unweighted path length from the root (germline) of the lineage tree, allowing for exclusion of specific groups of nodes.

Usage

getMRCA(
  graph,
  path = c("distance", "steps"),
  root = "Germline",
  field = NULL,
  exclude = NULL
)

Arguments

`graph`	igraph object containing an annotated lineage tree.
`path`	string defining whether to use unweighted (steps) or weighted (distance) measures for determining the founder node set..
`root`	name of the root (germline) node.
`field`	annotation field to use for both unweighted path length exclusion and consideration as an MRCA node. If `NULL` do not exclude any nodes.
`exclude`	vector of annotation values in `field` to exclude from the potential MRCA set. If `NULL` do not exclude any nodes. Has no effect if `field=NULL`.

Value

A data.frame of the MRCA node(s) containing the columns:

name: node name
steps: path length as the number of nodes traversed
distance: path length as the sum of edge weights

Along with additional columns corresponding to the annotations of the input graph.

Examples

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

# Use unweighted path length and do not exclude any nodes
getMRCA(graph, path="steps", root="Germline")

# Exclude nodes without an isotype annotation and use weighted path length
getMRCA(graph, path="distance", root="Germline", field="c_call", exclude=NA)