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Select a set of units from a cascade

Source: R/cascade_sets.R
dmsa_select.Rd

Choose one or more systems by short name. Everything below the system - modules, genes, probes - defaults to "full", meaning every unit the cascade assigns to the chosen system(s). Narrow a level only when the question is genuinely narrower, and note that narrowing changes the declared family and therefore the multiplicity toll.

Usage

dmsa_select(
  x = "alpha",
  systems = NULL,
  modules = "full",
  genes = "full",
  probes = "full",
  columns = NULL,
  data = NULL
)

Arguments

x

A dmsa_sets, or anything dmsa_sets() accepts.

systems

Short names (c("hpa", "oxytocin")), system ids, or full system names. NULL selects every system in the cascade. Matching is case-insensitive and accepts a unique prefix of a short name.

modules, genes, probes

"full" (default) or explicit ids/symbols to restrict to. modules takes module ids such as "2.6", genes takes symbols, probes takes CpG ids or probe ids.

columns

Which cascade column holds the data-matrix column names for this analysis - e.g. "col_parent_T1". "auto" picks the col_* column with the most overlap against data, when data is supplied. NULL leaves it unresolved.

data

Optional data.frame or matrix used by columns = "auto".

Value

An object of class dmsa_selection.

Examples

# \donttest{
sel <- dmsa_select(systems = c("hpa", "oxytocin"))
sel
#> dmsa selection from: Project Alpha 2026c (module-audited) 
#>   2 system(s) selected | modules full | genes full | probes full
#>    hpa              HPA axis & glucocorticoid signalling      8 mod    49 gene    538 cpg
#>    oxytocin         Oxytocin, vasopressin & CICR              9 mod    90 gene   1690 cpg
#>   total: 17 modules, 139 genes, 2228 CpGs
#>   module evidence: 17 High, 0 Moderate
#>   polarity: 110 signed, 29 off-axis (curated 52, database 10, literature 13, heuristic 62, none 2)
#>     35 row(s) need a decision - dmsa_polarity_review()
dmsa_select(systems = "hpa", modules = c("2.6", "2.8"))
#> dmsa selection from: Project Alpha 2026c (module-audited) 
#>   1 system(s) selected | modules restricted | genes full | probes full
#>    hpa              HPA axis & glucocorticoid signalling      2 mod    19 gene    154 cpg
#>   total: 2 modules, 19 genes, 154 CpGs
#>   module evidence: 2 High, 0 Moderate
#>   polarity: 14 signed, 5 off-axis (curated 11, database 1, heuristic 6, none 1)
#>     7 row(s) need a decision - dmsa_polarity_review()
# }