ag: Antigen
In acorg/acutilsLite: A package for working with CPE databases

Antigen

An antigen entry (ag) is an environment containing some of:

id	Antigen id: 6 random capital letters and numbers
strain	Rarely used.
long	Full strain name.
aliases	Other names known to be used to refer to this antigen.
wildtype	Boolean: whether the strain is wildtype.
type	Influenza virus type (A, B...)
subtype	Influenza virus subtype (H3N2, H1N1...)
lineage	Victoria etc
isolation	list containing isolation id, location, date, cell, continent
genes	gene sequence for HA/NA
parent_id	id of parent (by backbone)
.parent	the database entry for the parent antigen (by backbone)
alterations	alterations to parent (substitutions or gene transplants), organised by gene. Substitutions formatted as X123Y, transgenes identified by parent id. alterattion$.parent is the database entry for the gene origin when the alteration is a transplant.
passage	passaging history
comments	Extra comments - eg which study the antigen comes from
groups	Useful annotations. For example: wildtype, mutatant, gen 1 root, gen 2 mutant, 3C.3A etc.
meta	Some extra data about the antigen: cluster, mutant generation number, whether it is a reference strain

Notably, the parent environment is always the empty environment; $.parent is the backbone-wise parent antigen entry; alteration$.parent is the origin antigen for a transplanted gene

It has classes c("acdatabase.ag", "acdatabase.entry", "environment")

acorg/acutilsLite documentation built on Feb. 19, 2021, 4:56 p.m.