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Build a cascade tree for a set of probes from a reference bundle

Source: R/reference.R
dmsa_tree.Rd

Returns the tree argument dmsa_cascade() expects: one row per probe, columns ordered outermost first.

Usage

dmsa_tree(reference, genes, system_id = NULL, levels = NULL)

Arguments

reference

A dmsa_reference.

genes

Character vector, the set-membership gene of each probe.

system_id

Optional: restrict to one system (a gene can sit in several, which would otherwise duplicate probes).

levels

Which levels to include, in order. Defaults to c("system", "module") when a module layer exists, else "system". "gene" is always appended.

Value

data.frame with one row per probe. Probes whose gene is not in the reference get NA and should be routed to the flat unannotated arm.

Examples

systems <- data.frame(
  gene = c("CRH", "NR3C1", "FKBP5", "OXT"),
  system_id = c("HPA", "HPA", "HPA", "OXT"),
  system = c("HPA axis", "HPA axis", "HPA axis", "Oxytocin"),
  module_id = c("HPA.a", "HPA.b", "HPA.b", "OXT.a"),
  module = c("Drive", "Receptors", "Receptors", "Ligand"))
ref <- dmsa_reference(systems, anchor_method = "none")

## a probe whose gene is not in the bundle gets NA and goes to the flat arm
dmsa_tree(ref, genes = c("CRH", "NR3C1", "FKBP5", "NOTINSET"),
          system_id = "HPA")
#>   system module     gene
#> 1    HPA  HPA.a      CRH
#> 2    HPA  HPA.b    NR3C1
#> 3    HPA  HPA.b    FKBP5
#> 4   <NA>   <NA> NOTINSET