Retrieve norm_param from object.
norm_param(siamcat, errorIfNULL=TRUE) # S4 method for ANY norm_param(siamcat)
siamcat | (Required). An instance of siamcat-class that contains a norm_param |
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The norm_param list or NULL.
data(siamcat_example) norm_param(siamcat_example)#> $norm.method #> [1] "log.unit" #> #> $retained.feat #> [1] "unnamed.Ruminococcus.sp..SR1.5..u.1621." #> [2] "Eubacterium.rectale..h.1630." #> [3] "Eubacterium.hallii..h.1597." #> [4] "Eubacterium.ventriosum..h.1629." #> [5] "unnamed.Ruminococcaceae.bacterium.D16..u.1580." #> [6] "Eikenella.corrodens..h.448." #> [7] "Leptotrichia.hofstadii..h.1488." #> [8] "Peptostreptococcus.stomatis..h.1530." #> [9] "Fusobacterium.nucleatum..h.1480." #> [10] "Prevotella.nigrescens..h.1069." #> [11] "Porphyromonas.asaccharolytica..h.1056." #> [12] "Pseudoflavonifractor.capillosus..h.1579." #> [13] "Fusobacterium.nucleatum..h.1479." #> [14] "unclassified.Fusobacterium..c.1481." #> [15] "unclassified.Fusobacterium..c.1482." #> [16] "Neisseria.mucosa..h.436." #> [17] "Fusobacterium.gonidiaformans..h.1476." #> [18] "Collinsella.stercoris..h.812." #> [19] "unnamed.Azoarcus.sp..BH72..u.530." #> [20] "Aminomonas.paucivorans..h.1640." #> [21] "Lactobacillus.amylovorus..c.1447." #> [22] "unnamed.butyrate.producing.bacterium.SS3.4..u.1603." #> [23] "Streptococcus.australis..h.1420." #> [24] "Clostridium.saccharolyticum..h.1602." #> [25] "Salmonella.enterica..h.394." #> [26] "unnamed.Clostridium.sp..L2.50..u.1593." #> [27] "Mycobacterium.gilvum..h.859." #> [28] "Gallibacterium.anatis..h.328." #> [29] "Streptococcus.gallolyticus..c.1379." #> [30] "Variovorax.paradoxus..h.515." #> [31] "Tetragenococcus.halophilus..h.1367." #> [32] "unnamed.Clostridiales.bacterium.1_7_47FAA..u.1599." #> [33] "Desulfotomaculum.nigrificans..c.1680." #> [34] "Bacteroides.coprophilus..h.1106." #> [35] "Streptococcus.macacae..h.1374." #> [36] "Anaerococcus.tetradius..h.1499." #> [37] "unnamed.Citreicella.sp..SE45..u.625." #> [38] "Chromobacterium.violaceum..h.528." #> [39] "Anaeromyxobacter.dehalogenans..h.743." #> [40] "Pseudomonas.brassicacearum.fluorescens..c.233." #> [41] "Pseudomonas.syringae..h.229." #> [42] "Bifidobacterium.longum..h.970." #> [43] "Neptuniibacter.caesariensis..h.271." #> [44] "Burkholderia.cenocepacia..h.495." #> [45] "Rhodococcus.erythropolis..h.850." #> [46] "Streptococcus.parasanguinis..h.1421." #> [47] "Pseudomonas.mendocina..h.239." #> #> $log.n0 #> [1] 1e-06 #> #> $n.p #> [1] 2 #> #> $norm.margin #> [1] 1 #> #> $norm.fun #> function (x) #> { #> x/sqrt(sum(x^2)) #> } #> <bytecode: 0x11b4a0808> #> <environment: 0x11b4a64d8> #> #> $feat.norm.denom #> unnamed.Ruminococcus.sp..SR1.5..u.1621. #> 33.92765 #> Eubacterium.rectale..h.1630. #> 31.70352 #> Eubacterium.hallii..h.1597. #> 36.85332 #> Eubacterium.ventriosum..h.1629. #> 44.56123 #> unnamed.Ruminococcaceae.bacterium.D16..u.1580. #> 50.82967 #> Eikenella.corrodens..h.448. #> 70.48206 #> Leptotrichia.hofstadii..h.1488. #> 70.57224 #> Peptostreptococcus.stomatis..h.1530. #> 61.58349 #> Fusobacterium.nucleatum..h.1480. #> 67.92345 #> Prevotella.nigrescens..h.1069. #> 69.40454 #> Porphyromonas.asaccharolytica..h.1056. #> 68.40683 #> Pseudoflavonifractor.capillosus..h.1579. #> 50.53919 #> Fusobacterium.nucleatum..h.1479. #> 68.85390 #> unclassified.Fusobacterium..c.1481. #> 65.73738 #> unclassified.Fusobacterium..c.1482. #> 67.87579 #> Neisseria.mucosa..h.436. #> 70.47463 #> Fusobacterium.gonidiaformans..h.1476. #> 69.89933 #> Collinsella.stercoris..h.812. #> 65.17283 #> unnamed.Azoarcus.sp..BH72..u.530. #> 71.16803 #> Aminomonas.paucivorans..h.1640. #> 71.12320 #> Lactobacillus.amylovorus..c.1447. #> 70.62086 #> unnamed.butyrate.producing.bacterium.SS3.4..u.1603. #> 44.46898 #> Streptococcus.australis..h.1420. #> 53.73465 #> Clostridium.saccharolyticum..h.1602. #> 70.82718 #> Salmonella.enterica..h.394. #> 69.53648 #> unnamed.Clostridium.sp..L2.50..u.1593. #> 56.86779 #> Mycobacterium.gilvum..h.859. #> 71.20551 #> Gallibacterium.anatis..h.328. #> 70.93205 #> Streptococcus.gallolyticus..c.1379. #> 63.35816 #> Variovorax.paradoxus..h.515. #> 71.18818 #> Tetragenococcus.halophilus..h.1367. #> 71.10203 #> unnamed.Clostridiales.bacterium.1_7_47FAA..u.1599. #> 62.00783 #> Desulfotomaculum.nigrificans..c.1680. #> 71.20285 #> Bacteroides.coprophilus..h.1106. #> 65.06803 #> Streptococcus.macacae..h.1374. #> 71.13320 #> Anaerococcus.tetradius..h.1499. #> 71.21425 #> unnamed.Citreicella.sp..SE45..u.625. #> 71.20149 #> Chromobacterium.violaceum..h.528. #> 70.99082 #> Anaeromyxobacter.dehalogenans..h.743. #> 71.02467 #> Pseudomonas.brassicacearum.fluorescens..c.233. #> 70.95885 #> Pseudomonas.syringae..h.229. #> 71.13539 #> Bifidobacterium.longum..h.970. #> 41.62052 #> Neptuniibacter.caesariensis..h.271. #> 71.17762 #> Burkholderia.cenocepacia..h.495. #> 71.15968 #> Rhodococcus.erythropolis..h.850. #> 71.13074 #> Streptococcus.parasanguinis..h.1421. #> 45.61013 #> Pseudomonas.mendocina..h.239. #> 71.05295 #>