R: Combine IgPhyML object parameters into a dataframe

combineIgphyml {alakazam} | R Documentation

## Combine IgPhyML object parameters into a dataframe

### Description

`combineIgphyml` combines IgPhyML object parameters into a data.frame.

### Usage

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

### 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`.

### Value

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

### 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

    ## Not run:
       # 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))

    ## End(Not run)

[Package alakazam version 0.3.0 Index]