alakazam (version 1.3.0)

combineIgphyml: Combine IgPhyML object parameters into a dataframe

Description

combineIgphyml combines IgPhyML object parameters into a data.frame.

Usage

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

Value

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

Arguments

iglist

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.

format

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).

Details

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.

References

1. 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

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 https://doi.org/10.1101/558825

See Also

readIgphyml

Examples

if (FALSE) {
   # Read in and combine two igphyml runs
   s1 <- readIgphyml("IB+7d_lineages_gy.tsv_igphyml_stats_hlp.tab", id="+7d")
   s2 <- readIgphyml("IB+7d_lineages_gy.tsv_igphyml_stats_hlp.tab", id="s2")
   combineIgphyml(list(s1, s2))
}