The systems available in a cascade, with the short names to select them by
Source:R/cascade_sets.R
dmsa_systems.RdThe systems available in a cascade, with the short names to select them by
Arguments
- x
A
dmsa_setsordmsa_selection, or anythingdmsa_sets()accepts. A bare string that is neither"alpha"nor an existing file path is treated aspattern, sodmsa_systems("hpa")searches the bundled cascade.- pattern
Optional case-insensitive regular expression; matched against the short name, the full system name and the system id.
Value
A data.frame with system_id, system_short,
system and the module/gene/CpG counts. Printed as a table.
Examples
# \donttest{
dmsa_systems() # all 30
#> 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
dmsa_systems("stress|hpa") # search
#> system_id system_short system n_modules
#> 2 2 hpa HPA axis & glucocorticoid signalling 8
#> 29 29 oxidative Oxidative stress & mitochondria 6
#> n_genes n_cpgs
#> 2 49 538
#> 29 30 316
# }