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. IfNULL
do not exclude any nodes. Has no effect iffield=NULL
.
Value¶
A data.frame of the MRCA node(s) containing the columns:
name
: node namesteps
: path length as the number of nodes traverseddistance
: 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.