getMRCA - 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")


                         name
GN5SHBT06HH3QD GN5SHBT06HH3QD
                                                                                                                                                                                                                                                                                                                                                                                                                       sequence
GN5SHBT06HH3QD GAGGTGCAGCTGGTGGTATCTGGGGGANNNGGCTTGGTACAGCCAGGGCGGTCCCTAAGACTCTCCTGTACAGTTTCTGGATTCACCTTTNNNNNNNNNNNNGGTGATTATGCTATGACCTGGATCCGCCAGGCTCCTGGGAAGGGGCTGGAGTGGGTAGGTTTCATTAGAAGCAAAACTTTTGGTGGGACAGCAGATTACGCCGCGTTTGTGAGANNNGGCAGATTCACCATCTCAAGAGATGATTCCAAAAACATCGCCTATCTGCAATTGAACAGCCTGAAAACCGAGGACACAGGCGTCTATTACTGTGGTAGGGATCTCGCCGTAAGTGACACAATAGGTGGTACTAACTGGTTCGACCCCTGGGGCCAGGGGACCCCGGTCACCGTCTCCTCAG
               sample_id c_call duplicate_count          label steps distance
GN5SHBT06HH3QD       +7d   IGHA              10 GN5SHBT06HH3QD     1       20



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

                         name
GN5SHBT06HH3QD GN5SHBT06HH3QD
                                                                                                                                                                                                                                                                                                                                                                                                                       sequence
GN5SHBT06HH3QD GAGGTGCAGCTGGTGGTATCTGGGGGANNNGGCTTGGTACAGCCAGGGCGGTCCCTAAGACTCTCCTGTACAGTTTCTGGATTCACCTTTNNNNNNNNNNNNGGTGATTATGCTATGACCTGGATCCGCCAGGCTCCTGGGAAGGGGCTGGAGTGGGTAGGTTTCATTAGAAGCAAAACTTTTGGTGGGACAGCAGATTACGCCGCGTTTGTGAGANNNGGCAGATTCACCATCTCAAGAGATGATTCCAAAAACATCGCCTATCTGCAATTGAACAGCCTGAAAACCGAGGACACAGGCGTCTATTACTGTGGTAGGGATCTCGCCGTAAGTGACACAATAGGTGGTACTAACTGGTTCGACCCCTGGGGCCAGGGGACCCCGGTCACCGTCTCCTCAG
               sample_id c_call duplicate_count          label steps distance
GN5SHBT06HH3QD       +7d   IGHA              10 GN5SHBT06HH3QD     1       20

See also

Path lengths are determined with getPathLengths.