The cascade declares the analysis structure DMSA corrects within. Loading it is separate from loading a direction map: the cascade says which probes form which unit, the direction map says which way each probe points.
Arguments
- x
Either
"alpha"for the bundled, literature-audited Project Alpha 2026c cascade, a path to a CSV (optionally.gz) in the same shape, or adata.framealready in that shape. Seedmsa_sets_template()for the schema anddmsa_sets_check()to validate a file before use.- audit
Optional module-level evidence table: a path or
data.framewith one row permodule_idand any ofevidence_strength,audit_status,citation_keys,evidence_note,deep_search_url. Defaults to the bundled audit whenx = "alpha", and toNULLotherwise. When a user cascade already carries these columns they are used and no separate table is needed.- polarity
Optional gene-to-system polarity table (path,
data.frameordmsa_polarity) supplyingw_g. Defaults to the bundled Alpha polarity whenx = "alpha", to the cascade's ownw_gcolumn when it has one, and otherwise to none - in which case a system-level score weights every gene +1 and the print method says so. Usedmsa_polarity_fetch()to draft one for your own panel from public databases.- name
Optional label, printed and carried into reports.
See also
dmsa_systems() for the short names,
dmsa_select() to choose systems, dmsa_evidence() for the
module evidence table.
Examples
# \donttest{
cas <- dmsa_sets() # bundled Alpha 2026c
cas
#> dmsa selection cascade: Project Alpha 2026c (module-audited)
#> 30 systems | 188 modules | 1234 genes | 16823 CpGs | 17193 rows
#> data-column keys available: col_parent_T1, col_long, col_child_T4, col_child_maternal_T1, col_child_paternal_T1
#>
#> use these short names in systems = c(...):
#> 1 oxytocin Oxytocin, vasopressin & CICR 9 mod 90 gene 1690 cpg
#> 2 hpa HPA axis & glucocorticoid signalling 8 mod 49 gene 538 cpg
#> 3 steroidogenesis Steroidogenesis (adrenal & gonadal) 6 mod 35 gene 375 cpg
#> 4 sex_steroids Sex steroids: receptors & metabolism 8 mod 51 gene 698 cpg
#> 5 hpg HPG axis, puberty & KNDy 6 mod 55 gene 490 cpg
#> 6 libido Libido & sexual function 6 mod 33 gene 304 cpg
#> 7 pregnancy Pregnancy, parturition & lactation 6 mod 25 gene 222 cpg
#> 8 dopamine Dopamine 6 mod 34 gene 476 cpg
#> 9 serotonin Serotonin 7 mod 31 gene 300 cpg
#> 10 noradrenaline Noradrenaline & sympathetic nervous system 7 mod 31 gene 240 cpg
#> 11 monoamine Monoamine synthesis, transport & degradation 5 mod 19 gene 138 cpg
#> 12 opioid Opioid & melanocortin 5 mod 17 gene 201 cpg
#> 13 orexin Orexin / hypocretin & MCH 4 mod 14 gene 107 cpg
#> 14 endocannabinoid Endocannabinoid 4 mod 17 gene 204 cpg
#> 15 kynurenine Kynurenine pathway 5 mod 24 gene 338 cpg
#> 16 glutamate Glutamate & synaptic scaffolding 5 mod 61 gene 1533 cpg
#> 17 gaba GABA & excitation-inhibition balance 7 mod 43 gene 642 cpg
#> 18 neurotrophins Neurotrophins & activity-dependent plasticit 6 mod 48 gene 608 cpg
#> 19 gpcr GPCR signalling & second messengers 7 mod 40 gene 827 cpg
#> 20 epigenetic Epigenetic machinery 8 mod 87 gene 1250 cpg
#> 21 imprinted Imprinted genes & DMRs 6 mod 44 gene 703 cpg
#> 22 one_carbon One-carbon metabolism 8 mod 50 gene 438 cpg
#> 23 circadian Circadian & melatonin 5 mod 29 gene 336 cpg
#> 24 immune Immune, inflammation & HLA 13 mod 127 gene 1084 cpg
#> 25 social_synaptic Social-synaptic & psychiatric risk 5 mod 34 gene 1028 cpg
#> 26 thyroid Thyroid & neurodevelopment 6 mod 21 gene 328 cpg
#> 27 appetite Appetite & metabolic programming 7 mod 41 gene 795 cpg
#> 28 ageing Ageing, epigenetic clocks & telomere 4 mod 42 gene 602 cpg
#> 29 oxidative Oxidative stress & mitochondria 6 mod 30 gene 316 cpg
#> 30 pharmacogenes Pharmacogenes 3 mod 12 gene 74 cpg
#> module evidence: 163 High, 25 Moderate, 7 flagged (heterogeneous or measurement-defined)
#> dmsa_evidence() lists them with their citation keys
#> polarity: 874 signed, 360 off-axis (curated 112, database 191, literature 228, heuristic 676, none 27)
#> 190 row(s) need a decision - dmsa_polarity_review()
#>
#> dmsa_select(systems = c("oxytocin")) -> modules, genes and probes default to "full"
dmsa_systems() # the short names to use in `systems =`
#> system_id system_short system
#> 1 1 oxytocin Oxytocin, vasopressin & CICR
#> 2 2 hpa HPA axis & glucocorticoid signalling
#> 3 3 steroidogenesis Steroidogenesis (adrenal & gonadal)
#> 4 4 sex_steroids Sex steroids: receptors & metabolism
#> 5 5 hpg HPG axis, puberty & KNDy
#> 6 6 libido Libido & sexual function
#> 7 7 pregnancy Pregnancy, parturition & lactation
#> 8 8 dopamine Dopamine
#> 9 9 serotonin Serotonin
#> 10 10 noradrenaline Noradrenaline & sympathetic nervous system
#> 11 11 monoamine Monoamine synthesis, transport & degradation
#> 12 12 opioid Opioid & melanocortin
#> 13 13 orexin Orexin / hypocretin & MCH
#> 14 14 endocannabinoid Endocannabinoid
#> 15 15 kynurenine Kynurenine pathway
#> 16 16 glutamate Glutamate & synaptic scaffolding
#> 17 17 gaba GABA & excitation-inhibition balance
#> 18 18 neurotrophins Neurotrophins & activity-dependent plasticity
#> 19 19 gpcr GPCR signalling & second messengers
#> 20 20 epigenetic Epigenetic machinery
#> 21 21 imprinted Imprinted genes & DMRs
#> 22 22 one_carbon One-carbon metabolism
#> 23 23 circadian Circadian & melatonin
#> 24 24 immune Immune, inflammation & HLA
#> 25 25 social_synaptic Social-synaptic & psychiatric risk
#> 26 26 thyroid Thyroid & neurodevelopment
#> 27 27 appetite Appetite & metabolic programming
#> 28 28 ageing Ageing, epigenetic clocks & telomere
#> 29 29 oxidative Oxidative stress & mitochondria
#> 30 30 pharmacogenes Pharmacogenes
#> n_modules n_genes n_cpgs
#> 1 9 90 1690
#> 2 8 49 538
#> 3 6 35 375
#> 4 8 51 698
#> 5 6 55 490
#> 6 6 33 304
#> 7 6 25 222
#> 8 6 34 476
#> 9 7 31 300
#> 10 7 31 240
#> 11 5 19 138
#> 12 5 17 201
#> 13 4 14 107
#> 14 4 17 204
#> 15 5 24 338
#> 16 5 61 1533
#> 17 7 43 642
#> 18 6 48 608
#> 19 7 40 827
#> 20 8 87 1250
#> 21 6 44 703
#> 22 8 50 438
#> 23 5 29 336
#> 24 13 127 1084
#> 25 5 34 1028
#> 26 6 21 328
#> 27 7 41 795
#> 28 4 42 602
#> 29 6 30 316
#> 30 3 12 74
# }