Built-in population spec, derived from the supplied gating strategy
Source:R/populations.R
default_population_spec.RdThis is DATA, not code: each population is a list of (marker, direction) requirements evaluated against the resolved thresholds, all within the CD45+ parent. Users add or edit populations in the YAML config without touching R. A population whose markers are absent from the panel is reported UNAVAILABLE. This is a LITERAL transcription of the 15 populations in the gating strategy document, in document order. Each entry is (marker, direction) with direction one of "above", "below" or "intermediate". Nothing is added, renamed or inferred: populations the document does not list (e.g. dendritic cells, double-negative T cells, NKT cells) are deliberately absent, and gates the document specifies as double-positive are kept double-positive.
Details
lineage marks the three monocyte subsets, because the document scopes the
functional marker blocks by monocyte vs non-monocyte membership.
ONE DEPARTURE IN HOW, NOT WHAT. The regulatory T cell population keeps the
document's name and markers, but its CD25 and CD127 cuts are derived within
the CD3+ CD4+ T cells (parent:) rather than across every CD45+ cell. A
CD25 cut across all leukocytes falls wherever the CD25+ cells of every
lineage put it, and above it sit activated conventional T cells as well as
regulatory ones; the consensus gate is CD25+ CD127lo within CD4+ T cells
(Santegoets et al. 2015; Liu et al. 2006; Seddiki et al. 2006).