combineIgphyml {alakazam}R Documentation

Combine IgPhyML object parameters into a dataframe


combineIgphyml combines IgPhyML object parameters into a data.frame.


combineIgphyml(iglist, format = c("wide", "long"))



list of igphyml objects returned by readIgphyml. Each must have an id column in its param attribute, which can be added automatically using the id option of readIgphyml.


string specifying whether each column of the resulting data.frame should represent a parameter (wide) or if there should only be three columns; i.e. id, varable, and value (long).


combineIgphyml combines repertoire-wide parameter estimates from mutliple igphyml objects produced by readIgphyml into a dataframe that can be easily used for plotting and other hypothesis testing analyses.

All igphyml objects used must have an "id" column in their param attribute, which can be added automatically from the id flag of readIgphyml.


A data.frame containing HLP model parameter estimates for all igphyml objects. Only parameters shared among all objects will be returned.


  1. Hoehn KB, Lunter G, Pybus OG - A Phylogenetic Codon Substitution Model for Antibody Lineages. Genetics 2017 206(1):417-427

  2. 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

See Also



## Not run: 
   # Read in and combine two igphyml runs
   s1 <- readIgphyml("", id="+7d")
   s2 <- readIgphyml("", id="s2")
   combineIgphyml(list(s1, s2))

## End(Not run)

[Package alakazam version 1.1.0 Index]