readIgphyml reads output from the IgPhyML phylogenetics inference package for
B cell repertoires
readIgphyml(
file,
id = NULL,
format = c("graph", "phylo"),
collapse = FALSE,
branches = c("mutations", "distance")
)A list containing IgPhyML model parameters and estimated lineage trees.
Object attributes:
param: Data.frame of parameter estimates for each clonal
lineage. Columns include: CLONE, which is the
clone id; NSEQ, the total number of sequences in
the lineage; NSITE, the number of codon sites;
TREE_LENGTH, the sum of all branch lengths in
the estimated lineage tree; and LHOOD, the log
likelihood of the clone's sequences given the tree and
parameters. Subsequent columns are parameter estimates
from IgPhyML, which will depend on the model used.
Parameter columns ending with _MLE are maximum
likelihood estimates; those ending with _LCI are
the lower 95
with _UCI are the upper 95
estimate. The first line of param is for clone
REPERTOIRE,
which is a summary of all lineages within the repertoire.
For this row, NSEQ is the total number of sequences,
NSITE is the average number of sites, and
TREE_LENGTH is the mean tree length. For most
applications, parameter values will be the same for all
lineages within the repertoire, so access them simply by:
<object>$param$OMEGA_CDR_MLE[1] to, for instance,
get the estimate of dN/dS on the CDRs at the repertoire level.
trees: List of tree objects estimated by IgPhyML. If
format="graph" these are igraph graph objects.
If format="phylo", these are ape phylo objects.
command: Command used to run IgPhyML.
IgPhyML output file (.tab).
ID to assign to output object.
if "graph" return trees as igraph graph objects.
if "phylo" return trees as ape phylo objects.
if TRUE transform branch lengths to units of substitutions,
rather than substitutions per site, and collapse internal nodes
separated by branches < 0.1 substitutions. Will also remove all
internal node labels, as it makes them inconsistent.
if "distance" branch lengths are in expected mutations per
site. If "mutations" branches are in expected mutations.
readIgphyml reads output from the IgPhyML repertoire phylogenetics inference package.
The resulting object is divded between parameter estimates (usually under the HLP19 model),
which provide information about mutation and selection pressure operating on the sequences.
Trees returned from this function are either igraph objects or phylo objects, and each may be visualized accordingly. Futher, branch lengths in tree may represent either the expected number of substitutions per site (codon, if estimated under HLP or GY94 models), or the total number of expected substitutions per site. If the latter, internal nodes - but not tips - separated by branch lengths less than 0.1 are collapsed to simplify viewing.
Hoehn KB, Lunter G, Pybus OG - A Phylogenetic Codon Substitution Model for Antibody Lineages. Genetics 2017 206(1):417-427 https://doi.org/10.1534/genetics.116.196303
Hoehn KB, Vander Heiden JA, Zhou JQ, Lunter G, Pybus OG, Kleinstein SHK - Repertoire-wide phylogenetic models of B cell molecular evolution reveal evolutionary signatures of aging and vaccination. bioRxiv 2019 https://doi.org/10.1101/558825
if (FALSE) {
# Read in and plot a tree from an igphyml run
library(igraph)
s1 <- readIgphyml("IB+7d_lineages_gy.tsv_igphyml_stats_hlp.tab", id="+7d")
print(s1$param$OMEGA_CDR_MLE[1])
plot(s1$trees[[1]], layout=layout_as_tree, edge.label=E(s1$trees[[1]])$weight)
}
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