miga-base 1.2.15.2 → 1.2.15.4

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Files changed (306) hide show
  1. checksums.yaml +4 -4
  2. data/lib/miga/cli/action/download/gtdb.rb +4 -1
  3. data/lib/miga/cli/action/gtdb_get.rb +4 -0
  4. data/lib/miga/daemon.rb +4 -1
  5. data/lib/miga/lair.rb +6 -4
  6. data/lib/miga/remote_dataset/download.rb +3 -2
  7. data/lib/miga/remote_dataset.rb +25 -7
  8. data/lib/miga/taxonomy.rb +6 -0
  9. data/lib/miga/version.rb +2 -2
  10. metadata +6 -302
  11. data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Archaea_SCG.hmm +0 -41964
  12. data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Bacteria_SCG.hmm +0 -32439
  13. data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Complete_SCG_DB.hmm +0 -62056
  14. data/utils/FastAAI/FastAAI +0 -3659
  15. data/utils/FastAAI/FastAAI-legacy/FastAAI +0 -1336
  16. data/utils/FastAAI/FastAAI-legacy/kAAI_v1.0_virus.py +0 -1296
  17. data/utils/FastAAI/README.md +0 -84
  18. data/utils/enveomics/Docs/recplot2.md +0 -244
  19. data/utils/enveomics/Examples/aai-matrix.bash +0 -66
  20. data/utils/enveomics/Examples/ani-matrix.bash +0 -66
  21. data/utils/enveomics/Examples/essential-phylogeny.bash +0 -105
  22. data/utils/enveomics/Examples/unus-genome-phylogeny.bash +0 -100
  23. data/utils/enveomics/LICENSE.txt +0 -73
  24. data/utils/enveomics/Makefile +0 -52
  25. data/utils/enveomics/Manifest/Tasks/aasubs.json +0 -103
  26. data/utils/enveomics/Manifest/Tasks/blasttab.json +0 -790
  27. data/utils/enveomics/Manifest/Tasks/distances.json +0 -161
  28. data/utils/enveomics/Manifest/Tasks/fasta.json +0 -802
  29. data/utils/enveomics/Manifest/Tasks/fastq.json +0 -291
  30. data/utils/enveomics/Manifest/Tasks/graphics.json +0 -126
  31. data/utils/enveomics/Manifest/Tasks/mapping.json +0 -137
  32. data/utils/enveomics/Manifest/Tasks/ogs.json +0 -382
  33. data/utils/enveomics/Manifest/Tasks/other.json +0 -906
  34. data/utils/enveomics/Manifest/Tasks/remote.json +0 -355
  35. data/utils/enveomics/Manifest/Tasks/sequence-identity.json +0 -650
  36. data/utils/enveomics/Manifest/Tasks/tables.json +0 -308
  37. data/utils/enveomics/Manifest/Tasks/trees.json +0 -68
  38. data/utils/enveomics/Manifest/Tasks/variants.json +0 -111
  39. data/utils/enveomics/Manifest/categories.json +0 -165
  40. data/utils/enveomics/Manifest/examples.json +0 -162
  41. data/utils/enveomics/Manifest/tasks.json +0 -4
  42. data/utils/enveomics/Pipelines/assembly.pbs/CONFIG.mock.bash +0 -69
  43. data/utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl +0 -1
  44. data/utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl +0 -1
  45. data/utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl +0 -1
  46. data/utils/enveomics/Pipelines/assembly.pbs/README.md +0 -189
  47. data/utils/enveomics/Pipelines/assembly.pbs/RUNME-2.bash +0 -112
  48. data/utils/enveomics/Pipelines/assembly.pbs/RUNME-3.bash +0 -23
  49. data/utils/enveomics/Pipelines/assembly.pbs/RUNME-4.bash +0 -44
  50. data/utils/enveomics/Pipelines/assembly.pbs/RUNME.bash +0 -50
  51. data/utils/enveomics/Pipelines/assembly.pbs/kSelector.R +0 -37
  52. data/utils/enveomics/Pipelines/assembly.pbs/newbler.pbs +0 -68
  53. data/utils/enveomics/Pipelines/assembly.pbs/newbler_preparator.pl +0 -49
  54. data/utils/enveomics/Pipelines/assembly.pbs/soap.pbs +0 -80
  55. data/utils/enveomics/Pipelines/assembly.pbs/stats.pbs +0 -57
  56. data/utils/enveomics/Pipelines/assembly.pbs/velvet.pbs +0 -63
  57. data/utils/enveomics/Pipelines/blast.pbs/01.pbs.bash +0 -38
  58. data/utils/enveomics/Pipelines/blast.pbs/02.pbs.bash +0 -73
  59. data/utils/enveomics/Pipelines/blast.pbs/03.pbs.bash +0 -21
  60. data/utils/enveomics/Pipelines/blast.pbs/BlastTab.recover_job.pl +0 -72
  61. data/utils/enveomics/Pipelines/blast.pbs/CONFIG.mock.bash +0 -98
  62. data/utils/enveomics/Pipelines/blast.pbs/FastA.split.pl +0 -1
  63. data/utils/enveomics/Pipelines/blast.pbs/README.md +0 -127
  64. data/utils/enveomics/Pipelines/blast.pbs/RUNME.bash +0 -109
  65. data/utils/enveomics/Pipelines/blast.pbs/TASK.check.bash +0 -128
  66. data/utils/enveomics/Pipelines/blast.pbs/TASK.dry.bash +0 -16
  67. data/utils/enveomics/Pipelines/blast.pbs/TASK.eo.bash +0 -22
  68. data/utils/enveomics/Pipelines/blast.pbs/TASK.pause.bash +0 -26
  69. data/utils/enveomics/Pipelines/blast.pbs/TASK.run.bash +0 -89
  70. data/utils/enveomics/Pipelines/blast.pbs/sentinel.pbs.bash +0 -29
  71. data/utils/enveomics/Pipelines/idba.pbs/README.md +0 -49
  72. data/utils/enveomics/Pipelines/idba.pbs/RUNME.bash +0 -95
  73. data/utils/enveomics/Pipelines/idba.pbs/run.pbs +0 -56
  74. data/utils/enveomics/Pipelines/trim.pbs/README.md +0 -54
  75. data/utils/enveomics/Pipelines/trim.pbs/RUNME.bash +0 -70
  76. data/utils/enveomics/Pipelines/trim.pbs/run.pbs +0 -130
  77. data/utils/enveomics/README.md +0 -42
  78. data/utils/enveomics/Scripts/AAsubs.log2ratio.rb +0 -171
  79. data/utils/enveomics/Scripts/Aln.cat.rb +0 -221
  80. data/utils/enveomics/Scripts/Aln.convert.pl +0 -35
  81. data/utils/enveomics/Scripts/AlphaDiversity.pl +0 -152
  82. data/utils/enveomics/Scripts/BedGraph.tad.rb +0 -93
  83. data/utils/enveomics/Scripts/BedGraph.window.rb +0 -71
  84. data/utils/enveomics/Scripts/BlastPairwise.AAsubs.pl +0 -102
  85. data/utils/enveomics/Scripts/BlastTab.addlen.rb +0 -63
  86. data/utils/enveomics/Scripts/BlastTab.advance.bash +0 -48
  87. data/utils/enveomics/Scripts/BlastTab.best_hit_sorted.pl +0 -55
  88. data/utils/enveomics/Scripts/BlastTab.catsbj.pl +0 -104
  89. data/utils/enveomics/Scripts/BlastTab.cogCat.rb +0 -76
  90. data/utils/enveomics/Scripts/BlastTab.filter.pl +0 -47
  91. data/utils/enveomics/Scripts/BlastTab.kegg_pep2path_rest.pl +0 -194
  92. data/utils/enveomics/Scripts/BlastTab.metaxaPrep.pl +0 -104
  93. data/utils/enveomics/Scripts/BlastTab.pairedHits.rb +0 -157
  94. data/utils/enveomics/Scripts/BlastTab.recplot2.R +0 -48
  95. data/utils/enveomics/Scripts/BlastTab.seqdepth.pl +0 -86
  96. data/utils/enveomics/Scripts/BlastTab.seqdepth_ZIP.pl +0 -119
  97. data/utils/enveomics/Scripts/BlastTab.seqdepth_nomedian.pl +0 -86
  98. data/utils/enveomics/Scripts/BlastTab.subsample.pl +0 -47
  99. data/utils/enveomics/Scripts/BlastTab.sumPerHit.pl +0 -114
  100. data/utils/enveomics/Scripts/BlastTab.taxid2taxrank.pl +0 -90
  101. data/utils/enveomics/Scripts/BlastTab.topHits_sorted.rb +0 -123
  102. data/utils/enveomics/Scripts/Chao1.pl +0 -97
  103. data/utils/enveomics/Scripts/CharTable.classify.rb +0 -234
  104. data/utils/enveomics/Scripts/EBIseq2tax.rb +0 -83
  105. data/utils/enveomics/Scripts/FastA.N50.pl +0 -60
  106. data/utils/enveomics/Scripts/FastA.extract.rb +0 -152
  107. data/utils/enveomics/Scripts/FastA.filter.pl +0 -52
  108. data/utils/enveomics/Scripts/FastA.filterLen.pl +0 -28
  109. data/utils/enveomics/Scripts/FastA.filterN.pl +0 -60
  110. data/utils/enveomics/Scripts/FastA.fragment.rb +0 -100
  111. data/utils/enveomics/Scripts/FastA.gc.pl +0 -42
  112. data/utils/enveomics/Scripts/FastA.interpose.pl +0 -93
  113. data/utils/enveomics/Scripts/FastA.length.pl +0 -38
  114. data/utils/enveomics/Scripts/FastA.mask.rb +0 -89
  115. data/utils/enveomics/Scripts/FastA.per_file.pl +0 -36
  116. data/utils/enveomics/Scripts/FastA.qlen.pl +0 -57
  117. data/utils/enveomics/Scripts/FastA.rename.pl +0 -65
  118. data/utils/enveomics/Scripts/FastA.revcom.pl +0 -23
  119. data/utils/enveomics/Scripts/FastA.sample.rb +0 -98
  120. data/utils/enveomics/Scripts/FastA.slider.pl +0 -85
  121. data/utils/enveomics/Scripts/FastA.split.pl +0 -55
  122. data/utils/enveomics/Scripts/FastA.split.rb +0 -79
  123. data/utils/enveomics/Scripts/FastA.subsample.pl +0 -131
  124. data/utils/enveomics/Scripts/FastA.tag.rb +0 -65
  125. data/utils/enveomics/Scripts/FastA.toFastQ.rb +0 -69
  126. data/utils/enveomics/Scripts/FastA.wrap.rb +0 -48
  127. data/utils/enveomics/Scripts/FastQ.filter.pl +0 -54
  128. data/utils/enveomics/Scripts/FastQ.interpose.pl +0 -90
  129. data/utils/enveomics/Scripts/FastQ.maskQual.rb +0 -89
  130. data/utils/enveomics/Scripts/FastQ.offset.pl +0 -90
  131. data/utils/enveomics/Scripts/FastQ.split.pl +0 -53
  132. data/utils/enveomics/Scripts/FastQ.tag.rb +0 -70
  133. data/utils/enveomics/Scripts/FastQ.test-error.rb +0 -81
  134. data/utils/enveomics/Scripts/FastQ.toFastA.awk +0 -24
  135. data/utils/enveomics/Scripts/GFF.catsbj.pl +0 -127
  136. data/utils/enveomics/Scripts/GenBank.add_fields.rb +0 -84
  137. data/utils/enveomics/Scripts/HMM.essential.rb +0 -351
  138. data/utils/enveomics/Scripts/HMM.haai.rb +0 -168
  139. data/utils/enveomics/Scripts/HMMsearch.extractIds.rb +0 -83
  140. data/utils/enveomics/Scripts/JPlace.distances.rb +0 -88
  141. data/utils/enveomics/Scripts/JPlace.to_iToL.rb +0 -320
  142. data/utils/enveomics/Scripts/M5nr.getSequences.rb +0 -81
  143. data/utils/enveomics/Scripts/MeTaxa.distribution.pl +0 -198
  144. data/utils/enveomics/Scripts/MyTaxa.fragsByTax.pl +0 -35
  145. data/utils/enveomics/Scripts/MyTaxa.seq-taxrank.rb +0 -49
  146. data/utils/enveomics/Scripts/NCBIacc2tax.rb +0 -92
  147. data/utils/enveomics/Scripts/Newick.autoprune.R +0 -27
  148. data/utils/enveomics/Scripts/RAxML-EPA.to_iToL.pl +0 -228
  149. data/utils/enveomics/Scripts/RecPlot2.compareIdentities.R +0 -32
  150. data/utils/enveomics/Scripts/RefSeq.download.bash +0 -48
  151. data/utils/enveomics/Scripts/SRA.download.bash +0 -55
  152. data/utils/enveomics/Scripts/TRIBS.plot-test.R +0 -36
  153. data/utils/enveomics/Scripts/TRIBS.test.R +0 -39
  154. data/utils/enveomics/Scripts/Table.barplot.R +0 -31
  155. data/utils/enveomics/Scripts/Table.df2dist.R +0 -30
  156. data/utils/enveomics/Scripts/Table.filter.pl +0 -61
  157. data/utils/enveomics/Scripts/Table.merge.pl +0 -77
  158. data/utils/enveomics/Scripts/Table.prefScore.R +0 -60
  159. data/utils/enveomics/Scripts/Table.replace.rb +0 -69
  160. data/utils/enveomics/Scripts/Table.round.rb +0 -63
  161. data/utils/enveomics/Scripts/Table.split.pl +0 -57
  162. data/utils/enveomics/Scripts/Taxonomy.silva2ncbi.rb +0 -227
  163. data/utils/enveomics/Scripts/VCF.KaKs.rb +0 -147
  164. data/utils/enveomics/Scripts/VCF.SNPs.rb +0 -88
  165. data/utils/enveomics/Scripts/aai.rb +0 -421
  166. data/utils/enveomics/Scripts/ani.rb +0 -362
  167. data/utils/enveomics/Scripts/anir.rb +0 -137
  168. data/utils/enveomics/Scripts/clust.rand.rb +0 -102
  169. data/utils/enveomics/Scripts/gi2tax.rb +0 -103
  170. data/utils/enveomics/Scripts/in_silico_GA_GI.pl +0 -96
  171. data/utils/enveomics/Scripts/lib/data/dupont_2012_essential.hmm.gz +0 -0
  172. data/utils/enveomics/Scripts/lib/data/lee_2019_essential.hmm.gz +0 -0
  173. data/utils/enveomics/Scripts/lib/enveomics.R +0 -1
  174. data/utils/enveomics/Scripts/lib/enveomics_rb/anir.rb +0 -293
  175. data/utils/enveomics/Scripts/lib/enveomics_rb/bm_set.rb +0 -175
  176. data/utils/enveomics/Scripts/lib/enveomics_rb/enveomics.rb +0 -24
  177. data/utils/enveomics/Scripts/lib/enveomics_rb/errors.rb +0 -17
  178. data/utils/enveomics/Scripts/lib/enveomics_rb/gmm_em.rb +0 -30
  179. data/utils/enveomics/Scripts/lib/enveomics_rb/jplace.rb +0 -253
  180. data/utils/enveomics/Scripts/lib/enveomics_rb/match.rb +0 -88
  181. data/utils/enveomics/Scripts/lib/enveomics_rb/og.rb +0 -182
  182. data/utils/enveomics/Scripts/lib/enveomics_rb/rbm.rb +0 -49
  183. data/utils/enveomics/Scripts/lib/enveomics_rb/remote_data.rb +0 -74
  184. data/utils/enveomics/Scripts/lib/enveomics_rb/seq_range.rb +0 -237
  185. data/utils/enveomics/Scripts/lib/enveomics_rb/stats/rand.rb +0 -31
  186. data/utils/enveomics/Scripts/lib/enveomics_rb/stats/sample.rb +0 -152
  187. data/utils/enveomics/Scripts/lib/enveomics_rb/stats.rb +0 -3
  188. data/utils/enveomics/Scripts/lib/enveomics_rb/utils.rb +0 -74
  189. data/utils/enveomics/Scripts/lib/enveomics_rb/vcf.rb +0 -135
  190. data/utils/enveomics/Scripts/ogs.annotate.rb +0 -88
  191. data/utils/enveomics/Scripts/ogs.core-pan.rb +0 -160
  192. data/utils/enveomics/Scripts/ogs.extract.rb +0 -125
  193. data/utils/enveomics/Scripts/ogs.mcl.rb +0 -186
  194. data/utils/enveomics/Scripts/ogs.rb +0 -104
  195. data/utils/enveomics/Scripts/ogs.stats.rb +0 -131
  196. data/utils/enveomics/Scripts/rbm-legacy.rb +0 -172
  197. data/utils/enveomics/Scripts/rbm.rb +0 -108
  198. data/utils/enveomics/Scripts/sam.filter.rb +0 -148
  199. data/utils/enveomics/Tests/Makefile +0 -10
  200. data/utils/enveomics/Tests/Mgen_M2288.faa +0 -3189
  201. data/utils/enveomics/Tests/Mgen_M2288.fna +0 -8282
  202. data/utils/enveomics/Tests/Mgen_M2321.fna +0 -8288
  203. data/utils/enveomics/Tests/Nequ_Kin4M.faa +0 -2970
  204. data/utils/enveomics/Tests/Xanthomonas_oryzae-PilA.tribs.Rdata +0 -0
  205. data/utils/enveomics/Tests/Xanthomonas_oryzae-PilA.txt +0 -7
  206. data/utils/enveomics/Tests/Xanthomonas_oryzae.aai-mat.tsv +0 -17
  207. data/utils/enveomics/Tests/Xanthomonas_oryzae.aai.tsv +0 -137
  208. data/utils/enveomics/Tests/a_mg.cds-go.blast.tsv +0 -123
  209. data/utils/enveomics/Tests/a_mg.reads-cds.blast.tsv +0 -200
  210. data/utils/enveomics/Tests/a_mg.reads-cds.counts.tsv +0 -55
  211. data/utils/enveomics/Tests/alkB.nwk +0 -1
  212. data/utils/enveomics/Tests/anthrax-cansnp-data.tsv +0 -13
  213. data/utils/enveomics/Tests/anthrax-cansnp-key.tsv +0 -17
  214. data/utils/enveomics/Tests/hiv1.faa +0 -59
  215. data/utils/enveomics/Tests/hiv1.fna +0 -134
  216. data/utils/enveomics/Tests/hiv2.faa +0 -70
  217. data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv +0 -233
  218. data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.lim +0 -1
  219. data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.rec +0 -233
  220. data/utils/enveomics/Tests/phyla_counts.tsv +0 -10
  221. data/utils/enveomics/Tests/primate_lentivirus.ogs +0 -11
  222. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv1.rbm +0 -9
  223. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv2.rbm +0 -8
  224. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-siv.rbm +0 -6
  225. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-hiv2.rbm +0 -9
  226. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-siv.rbm +0 -6
  227. data/utils/enveomics/Tests/primate_lentivirus.rbm/siv-siv.rbm +0 -6
  228. data/utils/enveomics/build_enveomics_r.bash +0 -45
  229. data/utils/enveomics/enveomics.R/DESCRIPTION +0 -31
  230. data/utils/enveomics/enveomics.R/NAMESPACE +0 -39
  231. data/utils/enveomics/enveomics.R/R/autoprune.R +0 -155
  232. data/utils/enveomics/enveomics.R/R/barplot.R +0 -184
  233. data/utils/enveomics/enveomics.R/R/cliopts.R +0 -135
  234. data/utils/enveomics/enveomics.R/R/df2dist.R +0 -154
  235. data/utils/enveomics/enveomics.R/R/growthcurve.R +0 -331
  236. data/utils/enveomics/enveomics.R/R/prefscore.R +0 -79
  237. data/utils/enveomics/enveomics.R/R/recplot.R +0 -354
  238. data/utils/enveomics/enveomics.R/R/recplot2.R +0 -1631
  239. data/utils/enveomics/enveomics.R/R/tribs.R +0 -583
  240. data/utils/enveomics/enveomics.R/R/utils.R +0 -80
  241. data/utils/enveomics/enveomics.R/README.md +0 -81
  242. data/utils/enveomics/enveomics.R/data/growth.curves.rda +0 -0
  243. data/utils/enveomics/enveomics.R/data/phyla.counts.rda +0 -0
  244. data/utils/enveomics/enveomics.R/man/cash-enve.GrowthCurve-method.Rd +0 -16
  245. data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2-method.Rd +0 -16
  246. data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2.Peak-method.Rd +0 -16
  247. data/utils/enveomics/enveomics.R/man/enve.GrowthCurve-class.Rd +0 -25
  248. data/utils/enveomics/enveomics.R/man/enve.TRIBS-class.Rd +0 -46
  249. data/utils/enveomics/enveomics.R/man/enve.TRIBS.merge.Rd +0 -23
  250. data/utils/enveomics/enveomics.R/man/enve.TRIBStest-class.Rd +0 -47
  251. data/utils/enveomics/enveomics.R/man/enve.__prune.iter.Rd +0 -23
  252. data/utils/enveomics/enveomics.R/man/enve.__prune.reduce.Rd +0 -23
  253. data/utils/enveomics/enveomics.R/man/enve.__tribs.Rd +0 -40
  254. data/utils/enveomics/enveomics.R/man/enve.barplot.Rd +0 -103
  255. data/utils/enveomics/enveomics.R/man/enve.cliopts.Rd +0 -67
  256. data/utils/enveomics/enveomics.R/man/enve.col.alpha.Rd +0 -24
  257. data/utils/enveomics/enveomics.R/man/enve.col2alpha.Rd +0 -19
  258. data/utils/enveomics/enveomics.R/man/enve.df2dist.Rd +0 -45
  259. data/utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd +0 -44
  260. data/utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd +0 -47
  261. data/utils/enveomics/enveomics.R/man/enve.growthcurve.Rd +0 -75
  262. data/utils/enveomics/enveomics.R/man/enve.prefscore.Rd +0 -50
  263. data/utils/enveomics/enveomics.R/man/enve.prune.dist.Rd +0 -44
  264. data/utils/enveomics/enveomics.R/man/enve.recplot.Rd +0 -139
  265. data/utils/enveomics/enveomics.R/man/enve.recplot2-class.Rd +0 -45
  266. data/utils/enveomics/enveomics.R/man/enve.recplot2.ANIr.Rd +0 -24
  267. data/utils/enveomics/enveomics.R/man/enve.recplot2.Rd +0 -77
  268. data/utils/enveomics/enveomics.R/man/enve.recplot2.__counts.Rd +0 -25
  269. data/utils/enveomics/enveomics.R/man/enve.recplot2.__peakHist.Rd +0 -21
  270. data/utils/enveomics/enveomics.R/man/enve.recplot2.__whichClosestPeak.Rd +0 -19
  271. data/utils/enveomics/enveomics.R/man/enve.recplot2.changeCutoff.Rd +0 -19
  272. data/utils/enveomics/enveomics.R/man/enve.recplot2.compareIdentities.Rd +0 -47
  273. data/utils/enveomics/enveomics.R/man/enve.recplot2.coordinates.Rd +0 -29
  274. data/utils/enveomics/enveomics.R/man/enve.recplot2.corePeak.Rd +0 -18
  275. data/utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd +0 -45
  276. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.Rd +0 -36
  277. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_e.Rd +0 -19
  278. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_m.Rd +0 -19
  279. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__emauto_one.Rd +0 -27
  280. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mow_one.Rd +0 -52
  281. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mower.Rd +0 -17
  282. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.em.Rd +0 -51
  283. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.emauto.Rd +0 -43
  284. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.mower.Rd +0 -82
  285. data/utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd +0 -59
  286. data/utils/enveomics/enveomics.R/man/enve.recplot2.seqdepth.Rd +0 -27
  287. data/utils/enveomics/enveomics.R/man/enve.recplot2.windowDepthThreshold.Rd +0 -36
  288. data/utils/enveomics/enveomics.R/man/enve.selvector.Rd +0 -23
  289. data/utils/enveomics/enveomics.R/man/enve.tribs.Rd +0 -68
  290. data/utils/enveomics/enveomics.R/man/enve.tribs.test.Rd +0 -28
  291. data/utils/enveomics/enveomics.R/man/enve.truncate.Rd +0 -27
  292. data/utils/enveomics/enveomics.R/man/growth.curves.Rd +0 -14
  293. data/utils/enveomics/enveomics.R/man/phyla.counts.Rd +0 -13
  294. data/utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd +0 -78
  295. data/utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd +0 -46
  296. data/utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd +0 -45
  297. data/utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd +0 -125
  298. data/utils/enveomics/enveomics.R/man/summary.enve.GrowthCurve.Rd +0 -19
  299. data/utils/enveomics/enveomics.R/man/summary.enve.TRIBS.Rd +0 -19
  300. data/utils/enveomics/enveomics.R/man/summary.enve.TRIBStest.Rd +0 -19
  301. data/utils/enveomics/globals.mk +0 -8
  302. data/utils/enveomics/manifest.json +0 -9
  303. data/utils/multitrim/Multitrim How-To.pdf +0 -0
  304. data/utils/multitrim/README.md +0 -67
  305. data/utils/multitrim/multitrim.py +0 -1555
  306. data/utils/multitrim/multitrim.yml +0 -13
@@ -1,45 +0,0 @@
1
- % Generated by roxygen2: do not edit by hand
2
- % Please edit documentation in R/recplot2.R
3
- \name{enve.recplot2.extractWindows}
4
- \alias{enve.recplot2.extractWindows}
5
- \title{Enveomics: Recruitment Plot (2) Extract Windows}
6
- \usage{
7
- enve.recplot2.extractWindows(
8
- rp,
9
- peak,
10
- lower.tail = TRUE,
11
- significance = 0.05,
12
- seq.names = FALSE
13
- )
14
- }
15
- \arguments{
16
- \item{rp}{Recruitment plot, a \code{\link{enve.RecPlot2}} object.}
17
-
18
- \item{peak}{Peak, an \code{\link{enve.RecPlot2.Peak}} object. If list, it is assumed to be a
19
- list of \code{\link{enve.RecPlot2.Peak}} objects, in which case the core peak is
20
- used (see \code{\link{enve.recplot2.corePeak}}).}
21
-
22
- \item{lower.tail}{If \code{FALSE}, it returns windows significantly above the peak in
23
- sequencing depth.}
24
-
25
- \item{significance}{Significance threshold (alpha) to select windows.}
26
-
27
- \item{seq.names}{Returns subject sequence names instead of a vector of Booleans. If
28
- the recruitment plot was generated with named position bins (e.g, using
29
- \code{pos.breaks=0} or a two-column \code{pos.breaks.tsv}), it returns a
30
- vector of characters (the sequence identifiers), otherwise it returns a
31
- data.frame with a name column and two columns of coordinates.}
32
- }
33
- \value{
34
- Returns a vector of logicals if \code{seq.names = FALSE}.
35
- If \code{seq.names = TRUE}, it returns a data.frame with five columns:
36
- \code{name.from}, \code{name.to}, \code{pos.from}, \code{pos.to}, and
37
- \code{seq.name} (see \code{\link{enve.recplot2.coordinates}}).
38
- }
39
- \description{
40
- Extract windows significantly below (or above) the peak in sequencing
41
- depth.
42
- }
43
- \author{
44
- Luis M. Rodriguez-R [aut, cre]
45
- }
@@ -1,36 +0,0 @@
1
- % Generated by roxygen2: do not edit by hand
2
- % Please edit documentation in R/recplot2.R
3
- \name{enve.recplot2.findPeaks}
4
- \alias{enve.recplot2.findPeaks}
5
- \title{Enveomics: Recruitment Plot (2) Peak Finder}
6
- \usage{
7
- enve.recplot2.findPeaks(x, method = "emauto", ...)
8
- }
9
- \arguments{
10
- \item{x}{An \code{\link{enve.RecPlot2}} object.}
11
-
12
- \item{method}{Peak-finder method. This should be one of:
13
- \itemize{
14
- \item \strong{emauto}
15
- (Expectation-Maximization with auto-selection of components)
16
- \item \strong{em}
17
- (Expectation-Maximization)
18
- \item \strong{mower}
19
- (Custom distribution-mowing method)
20
- }}
21
-
22
- \item{...}{Any additional parameters supported by
23
- \code{\link{enve.recplot2.findPeaks}}.}
24
- }
25
- \value{
26
- Returns a list of \code{\link{enve.RecPlot2.Peak}} objects.
27
- }
28
- \description{
29
- Identifies peaks in the population histogram potentially indicating
30
- sub-population mixtures.
31
- }
32
- \author{
33
- Luis M. Rodriguez-R [aut, cre]
34
-
35
- export
36
- }
@@ -1,19 +0,0 @@
1
- % Generated by roxygen2: do not edit by hand
2
- % Please edit documentation in R/recplot2.R
3
- \name{enve.recplot2.findPeaks.__em_e}
4
- \alias{enve.recplot2.findPeaks.__em_e}
5
- \title{Enveomics: Recruitment Plot (2) EM Peak Finder - Internal Ancillary Function Expectation}
6
- \usage{
7
- enve.recplot2.findPeaks.__em_e(x, theta)
8
- }
9
- \arguments{
10
- \item{x}{Vector of log-transformed sequencing depths}
11
-
12
- \item{theta}{Parameters list}
13
- }
14
- \description{
15
- Internal ancillary function (see \code{\link{enve.recplot2.findPeaks.em}}).
16
- }
17
- \author{
18
- Luis M. Rodriguez-R [aut, cre]
19
- }
@@ -1,19 +0,0 @@
1
- % Generated by roxygen2: do not edit by hand
2
- % Please edit documentation in R/recplot2.R
3
- \name{enve.recplot2.findPeaks.__em_m}
4
- \alias{enve.recplot2.findPeaks.__em_m}
5
- \title{Enveomics: Recruitment Plot (2) Em Peak Finder - Internal Ancillary Function Maximization}
6
- \usage{
7
- enve.recplot2.findPeaks.__em_m(x, posterior)
8
- }
9
- \arguments{
10
- \item{x}{Vector of log-transformed sequencing depths}
11
-
12
- \item{posterior}{Posterior probability}
13
- }
14
- \description{
15
- Internal ancillary function (see \code{\link{enve.recplot2.findPeaks.em}}).
16
- }
17
- \author{
18
- Luis M. Rodriguez-R [aut, cre]
19
- }
@@ -1,27 +0,0 @@
1
- % Generated by roxygen2: do not edit by hand
2
- % Please edit documentation in R/recplot2.R
3
- \name{enve.recplot2.findPeaks.__emauto_one}
4
- \alias{enve.recplot2.findPeaks.__emauto_one}
5
- \title{Enveomics: Recruitment Plot (2) EMauto Peak Finder - Internal Ancillary Function}
6
- \usage{
7
- enve.recplot2.findPeaks.__emauto_one(x, comp, do_crit, best, verbose, ...)
8
- }
9
- \arguments{
10
- \item{x}{\code{\link{enve.RecPlot2}} object}
11
-
12
- \item{comp}{Components}
13
-
14
- \item{do_crit}{Function estimating the criterion}
15
-
16
- \item{best}{Best solution thus far}
17
-
18
- \item{verbose}{If verbose}
19
-
20
- \item{...}{Additional parameters for \code{\link{enve.recplot2.findPeaks.em}}}
21
- }
22
- \description{
23
- Internal ancillary function (see \code{\link{enve.recplot2.findPeaks.emauto}}).
24
- }
25
- \author{
26
- Luis M. Rodriguez-R [aut, cre]
27
- }
@@ -1,52 +0,0 @@
1
- % Generated by roxygen2: do not edit by hand
2
- % Please edit documentation in R/recplot2.R
3
- \name{enve.recplot2.findPeaks.__mow_one}
4
- \alias{enve.recplot2.findPeaks.__mow_one}
5
- \title{Enveomics: Recruitment Plot (2) Mowing Peak Finder - Internal Ancillary Function 1}
6
- \usage{
7
- enve.recplot2.findPeaks.__mow_one(
8
- lsd1,
9
- min.points,
10
- quant.est,
11
- mlv.opts,
12
- fitdist.opts,
13
- with.skewness,
14
- optim.rounds,
15
- optim.epsilon,
16
- n.total,
17
- merge.logdist,
18
- verbose,
19
- log
20
- )
21
- }
22
- \arguments{
23
- \item{lsd1}{Vector of log-transformed sequencing depths}
24
-
25
- \item{min.points}{Minimum number of points}
26
-
27
- \item{quant.est}{Quantile estimate}
28
-
29
- \item{mlv.opts}{List of options for \code{mlv}}
30
-
31
- \item{fitdist.opts}{List of options for \code{fitdist}}
32
-
33
- \item{with.skewness}{If skewed-normal should be used}
34
-
35
- \item{optim.rounds}{Maximum number of optimization rounds}
36
-
37
- \item{optim.epsilon}{Minimum difference considered negligible}
38
-
39
- \item{n.total}{Global number of windows}
40
-
41
- \item{merge.logdist}{Attempted \code{merge.logdist} parameter}
42
-
43
- \item{verbose}{If verbose}
44
-
45
- \item{log}{If log-transformed depths}
46
- }
47
- \description{
48
- Internall ancillary function (see \code{\link{enve.recplot2.findPeaks.mower}}).
49
- }
50
- \author{
51
- Luis M. Rodriguez-R [aut, cre]
52
- }
@@ -1,17 +0,0 @@
1
- % Generated by roxygen2: do not edit by hand
2
- % Please edit documentation in R/recplot2.R
3
- \name{enve.recplot2.findPeaks.__mower}
4
- \alias{enve.recplot2.findPeaks.__mower}
5
- \title{Enveomics: Recruitment Plot (2) Mowing Peak Finder - Internal Ancillary Function 2}
6
- \usage{
7
- enve.recplot2.findPeaks.__mower(peaks.opts)
8
- }
9
- \arguments{
10
- \item{peaks.opts}{List of options for \code{\link{enve.recplot2.findPeaks.__mow_one}}}
11
- }
12
- \description{
13
- Internal ancillary function (see \code{\link{enve.recplot2.findPeaks.mower}}).
14
- }
15
- \author{
16
- Luis M. Rodriguez-R [aut, cre]
17
- }
@@ -1,51 +0,0 @@
1
- % Generated by roxygen2: do not edit by hand
2
- % Please edit documentation in R/recplot2.R
3
- \name{enve.recplot2.findPeaks.em}
4
- \alias{enve.recplot2.findPeaks.em}
5
- \title{Enveomics: Recruitment Plot (2) Em Peak Finder}
6
- \usage{
7
- enve.recplot2.findPeaks.em(
8
- x,
9
- max.iter = 1000,
10
- ll.diff.res = 1e-08,
11
- components = 2,
12
- rm.top = 0.05,
13
- verbose = FALSE,
14
- init,
15
- log = TRUE
16
- )
17
- }
18
- \arguments{
19
- \item{x}{An \code{\link{enve.RecPlot2}} object.}
20
-
21
- \item{max.iter}{Maximum number of EM iterations.}
22
-
23
- \item{ll.diff.res}{Maximum Log-Likelihood difference to be considered as convergent.}
24
-
25
- \item{components}{Number of distributions assumed in the mixture.}
26
-
27
- \item{rm.top}{Top-values to remove before finding peaks, as a quantile probability.
28
- This step is useful to remove highly conserved regions, but can be
29
- turned off by setting \code{rm.top=0}. The quantile is determined
30
- \strong{after} removing zero-coverage windows.}
31
-
32
- \item{verbose}{Display (mostly debugging) information.}
33
-
34
- \item{init}{Initialization parameters. By default, these are derived from k-means
35
- clustering. A named list with vectors for \code{mu}, \code{sd}, and
36
- \code{alpha}, each of length \code{components}.}
37
-
38
- \item{log}{Logical value indicating if the estimations should be performed in
39
- natural logarithm units. Do not change unless you know what you're
40
- doing.}
41
- }
42
- \value{
43
- Returns a list of \code{\link{enve.RecPlot2.Peak}} objects.
44
- }
45
- \description{
46
- Identifies peaks in the population histogram using a Gaussian Mixture
47
- Model Expectation Maximization (GMM-EM) method.
48
- }
49
- \author{
50
- Luis M. Rodriguez-R [aut, cre]
51
- }
@@ -1,43 +0,0 @@
1
- % Generated by roxygen2: do not edit by hand
2
- % Please edit documentation in R/recplot2.R
3
- \name{enve.recplot2.findPeaks.emauto}
4
- \alias{enve.recplot2.findPeaks.emauto}
5
- \title{Enveomics: Recruitment Plot (2) Emauto Peak Finder}
6
- \usage{
7
- enve.recplot2.findPeaks.emauto(
8
- x,
9
- components = seq(1, 5),
10
- criterion = "aic",
11
- merge.tol = 2L,
12
- verbose = FALSE,
13
- ...
14
- )
15
- }
16
- \arguments{
17
- \item{x}{An \code{\link{enve.RecPlot2}} object.}
18
-
19
- \item{components}{A vector of number of components to evaluate.}
20
-
21
- \item{criterion}{Criterion to use for components selection. Must be one of:
22
- \code{aic} (Akaike Information Criterion), \code{bic} or \code{sbc}
23
- (Bayesian Information Criterion or Schwarz Criterion).}
24
-
25
- \item{merge.tol}{When attempting to merge peaks with very similar sequencing depth, use
26
- this number of significant digits (in log-scale).}
27
-
28
- \item{verbose}{Display (mostly debugging) information.}
29
-
30
- \item{...}{Any additional parameters supported by
31
- \code{\link{enve.recplot2.findPeaks.em}}.}
32
- }
33
- \value{
34
- Returns a list of \code{\link{enve.RecPlot2.Peak}} objects.
35
- }
36
- \description{
37
- Identifies peaks in the population histogram using a Gaussian Mixture
38
- Model Expectation Maximization (GMM-EM) method with number of components
39
- automatically detected.
40
- }
41
- \author{
42
- Luis M. Rodriguez-R [aut, cre]
43
- }
@@ -1,82 +0,0 @@
1
- % Generated by roxygen2: do not edit by hand
2
- % Please edit documentation in R/recplot2.R
3
- \name{enve.recplot2.findPeaks.mower}
4
- \alias{enve.recplot2.findPeaks.mower}
5
- \title{Enveomics: Recruitment Plot (2) Mowing Peak Finder}
6
- \usage{
7
- enve.recplot2.findPeaks.mower(
8
- x,
9
- min.points = 10,
10
- quant.est = c(0.002, 0.998),
11
- mlv.opts = list(method = "parzen"),
12
- fitdist.opts.sn = list(distr = "sn", method = "qme", probs = c(0.1, 0.5, 0.8), start =
13
- list(omega = 1, alpha = -1), lower = c(0, -Inf, -Inf)),
14
- fitdist.opts.norm = list(distr = "norm", method = "qme", probs = c(0.4, 0.6), start =
15
- list(sd = 1), lower = c(0, -Inf)),
16
- rm.top = 0.05,
17
- with.skewness = TRUE,
18
- optim.rounds = 200,
19
- optim.epsilon = 1e-04,
20
- merge.logdist = log(1.75),
21
- verbose = FALSE,
22
- log = TRUE
23
- )
24
- }
25
- \arguments{
26
- \item{x}{An \code{\link{enve.RecPlot2}} object.}
27
-
28
- \item{min.points}{Minimum number of points in the quantile-estimation-range
29
- \code{(quant.est)} to estimate a peak.}
30
-
31
- \item{quant.est}{Range of quantiles to be used in the estimation of a peak's
32
- parameters.}
33
-
34
- \item{mlv.opts}{Ignored. For backwards compatibility.}
35
-
36
- \item{fitdist.opts.sn}{Options passed to \code{fitdist} to estimate the standard deviation if
37
- \code{with.skewness=TRUE}. Note that the \code{start} parameter will be
38
- ammended with \code{xi=estimated} mode for each peak.}
39
-
40
- \item{fitdist.opts.norm}{Options passed to \code{fitdist} to estimate the standard deviation if
41
- \code{with.skewness=FALSE}. Note that the \code{start} parameter will be
42
- ammended with \code{mean=estimated} mode for each peak.}
43
-
44
- \item{rm.top}{Top-values to remove before finding peaks, as a quantile probability.
45
- This step is useful to remove highly conserved regions, but can be
46
- turned off by setting \code{rm.top=0}. The quantile is determined
47
- \strong{after} removing zero-coverage windows.}
48
-
49
- \item{with.skewness}{Allow skewness correction of the peaks. Typically, the
50
- sequencing-depth distribution for a single peak is left-skewed, due
51
- partly (but not exclusively) to fragmentation and mapping sensitivity.
52
- See \emph{Lindner et al 2013, Bioinformatics 29(10):1260-7} for an
53
- alternative solution for the first problem (fragmentation) called
54
- "tail distribution".}
55
-
56
- \item{optim.rounds}{Maximum rounds of peak optimization.}
57
-
58
- \item{optim.epsilon}{Trace change at which optimization stops (unless \code{optim.rounds} is
59
- reached first). The trace change is estimated as the sum of square
60
- differences between parameters in one round and those from two rounds
61
- earlier (to avoid infinite loops from approximation).}
62
-
63
- \item{merge.logdist}{Maximum value of \code{|log-ratio|} between centrality parameters in peaks
64
- to attempt merging. The default of ~0.22 corresponds to a maximum
65
- difference of 25\%.}
66
-
67
- \item{verbose}{Display (mostly debugging) information.}
68
-
69
- \item{log}{Logical value indicating if the estimations should be performed in
70
- natural logarithm units. Do not change unless you know what you're
71
- doing.}
72
- }
73
- \value{
74
- Returns a list of \code{\link{enve.RecPlot2.Peak}} objects.
75
- }
76
- \description{
77
- Identifies peaks in the population histogram potentially indicating
78
- sub-population mixtures, using a custom distribution-mowing method.
79
- }
80
- \author{
81
- Luis M. Rodriguez-R [aut, cre]
82
- }
@@ -1,59 +0,0 @@
1
- % Generated by roxygen2: do not edit by hand
2
- % Please edit documentation in R/recplot2.R
3
- \docType{class}
4
- \name{enve.RecPlot2.Peak-class}
5
- \alias{enve.RecPlot2.Peak-class}
6
- \alias{enve.RecPlot2.Peak}
7
- \title{Enveomics: Recruitment Plot (2) Peak - S4 Class}
8
- \description{
9
- Enve-omics representation of a peak in the sequencing depth histogram
10
- of a Recruitment plot (see \code{\link{enve.recplot2.findPeaks}}).
11
- }
12
- \section{Slots}{
13
-
14
- \describe{
15
- \item{\code{dist}}{\code{(character)}
16
- Distribution of the peak. Currently supported: \code{norm} (normal) and \code{sn}
17
- (skew-normal).}
18
-
19
- \item{\code{values}}{\code{(numeric)}
20
- Sequencing depth values predicted to conform the peak.}
21
-
22
- \item{\code{values.res}}{\code{(numeric)}
23
- Sequencing depth values not explained by this or previously identified
24
- peaks.}
25
-
26
- \item{\code{mode}}{\code{(numeric)}
27
- Seed-value of mode anchoring the peak.}
28
-
29
- \item{\code{param.hat}}{\code{(list)}
30
- Parameters of the distribution. A list of two values if dist=\code{norm} (sd
31
- and mean), or three values if dist=\code{sn}(omega=scale, alpha=shape, and
32
- xi=location). Note that the "dispersion" parameter is always first and
33
- the "location" parameter is always last.}
34
-
35
- \item{\code{n.hat}}{\code{(numeric)}
36
- Number of bins estimated to be explained by this peak. This should
37
- ideally be equal to the length of \code{values}, but it's not an integer.}
38
-
39
- \item{\code{n.total}}{\code{(numeric)}
40
- Total number of bins from which the peak was extracted. I.e., total
41
- number of position bins with non-zero sequencing depth in the recruitment
42
- plot (regardless of peak count).}
43
-
44
- \item{\code{err.res}}{\code{(numeric)}
45
- Error left after adding the peak (mower) or log-likelihood (em or emauto).}
46
-
47
- \item{\code{merge.logdist}}{\code{(numeric)}
48
- Attempted \code{merge.logdist} parameter.}
49
-
50
- \item{\code{seq.depth}}{\code{(numeric)}
51
- Best estimate available for the sequencing depth of the peak (centrality).}
52
-
53
- \item{\code{log}}{\code{(logical)}
54
- Indicates if the estimation was performed in natural logarithm space.}
55
- }}
56
-
57
- \author{
58
- Luis M. Rodriguez-R [aut, cre]
59
- }
@@ -1,27 +0,0 @@
1
- % Generated by roxygen2: do not edit by hand
2
- % Please edit documentation in R/recplot2.R
3
- \name{enve.recplot2.seqdepth}
4
- \alias{enve.recplot2.seqdepth}
5
- \title{Enveomics: Recruitment Plot (2) Sequencing Depth}
6
- \usage{
7
- enve.recplot2.seqdepth(x, sel, low.identity = FALSE)
8
- }
9
- \arguments{
10
- \item{x}{\code{\link{enve.RecPlot2}} object.}
11
-
12
- \item{sel}{Window(s) for which the sequencing depth is to be calculated. If not
13
- passed, it returns the sequencing depth of all windows.}
14
-
15
- \item{low.identity}{A logical indicating if the sequencing depth is to be estimated only
16
- with low-identity matches. By default, only high-identity matches are
17
- used.}
18
- }
19
- \value{
20
- Returns a numeric vector of sequencing depths (in bp/bp).
21
- }
22
- \description{
23
- Calculate the sequencing depth of the given window(s).
24
- }
25
- \author{
26
- Luis M. Rodriguez-R [aut, cre]
27
- }
@@ -1,36 +0,0 @@
1
- % Generated by roxygen2: do not edit by hand
2
- % Please edit documentation in R/recplot2.R
3
- \name{enve.recplot2.windowDepthThreshold}
4
- \alias{enve.recplot2.windowDepthThreshold}
5
- \title{Enveomics: Recruitment Plot (2) Window Depth Threshold}
6
- \usage{
7
- enve.recplot2.windowDepthThreshold(
8
- rp,
9
- peak,
10
- lower.tail = TRUE,
11
- significance = 0.05
12
- )
13
- }
14
- \arguments{
15
- \item{rp}{Recruitment plot, an \code{\link{enve.RecPlot2}} object.}
16
-
17
- \item{peak}{Peak, an \code{\link{enve.RecPlot2.Peak}} object. If list, it is assumed to be a
18
- list of \code{\link{enve.RecPlot2.Peak}} objects, in which case the core peak is
19
- used (see \code{\link{enve.recplot2.corePeak}}).}
20
-
21
- \item{lower.tail}{If \code{FALSE}, it returns windows significantly above the peak in
22
- sequencing depth.}
23
-
24
- \item{significance}{Significance threshold (alpha) to select windows.}
25
- }
26
- \value{
27
- Returns a float. The units are depth if the peaks were estimated in
28
- linear scale, or log-depth otherwise (\code{peak$log}).
29
- }
30
- \description{
31
- Identifies the threshold below which windows should be identified as
32
- variable or absent.
33
- }
34
- \author{
35
- Luis M. Rodriguez-R [aut, cre]
36
- }
@@ -1,23 +0,0 @@
1
- % Generated by roxygen2: do not edit by hand
2
- % Please edit documentation in R/utils.R
3
- \name{enve.selvector}
4
- \alias{enve.selvector}
5
- \title{Enveomics: Selection vector}
6
- \usage{
7
- enve.selvector(sel, dim.names)
8
- }
9
- \arguments{
10
- \item{sel}{A vector of numbers, characters, or booleans.}
11
-
12
- \item{dim.names}{A vector of names from which to select.}
13
- }
14
- \value{
15
- Returns a logical vector with the same length as \code{dim.name}.
16
- }
17
- \description{
18
- Normalizes a selection vector \code{sel} to a logical vector with indexes
19
- from \code{dim.names}.
20
- }
21
- \author{
22
- Luis M. Rodriguez-R [aut, cre]
23
- }
@@ -1,68 +0,0 @@
1
- % Generated by roxygen2: do not edit by hand
2
- % Please edit documentation in R/tribs.R
3
- \name{enve.tribs}
4
- \alias{enve.tribs}
5
- \title{Enveomics: TRIBS}
6
- \usage{
7
- enve.tribs(
8
- dist,
9
- selection = labels(dist),
10
- replicates = 1000,
11
- summary.fx = median,
12
- dist.method = "euclidean",
13
- subsamples = seq(0, 1, by = 0.01),
14
- dimensions = ceiling(length(selection) * 0.05),
15
- metaMDS.opts = list(),
16
- threads = 2,
17
- verbosity = 1,
18
- points,
19
- pre.tribs
20
- )
21
- }
22
- \arguments{
23
- \item{dist}{Distances as a \code{dist} object.}
24
-
25
- \item{selection}{Objects to include in the subsample. By default, all objects are
26
- selected.}
27
-
28
- \item{replicates}{Number of replications per point.}
29
-
30
- \item{summary.fx}{Function to summarize the distance distributions in a given replicate. By
31
- default, the median distance is estimated.}
32
-
33
- \item{dist.method}{Distance method between random points and samples in the transformed
34
- space. See \code{dist}.}
35
-
36
- \item{subsamples}{Subsampling fractions.}
37
-
38
- \item{dimensions}{Dimensions to use in the NMDS. By default, 5\% of the selection length.}
39
-
40
- \item{metaMDS.opts}{Any additional options to pass to metaMDS, as \code{list}.}
41
-
42
- \item{threads}{Number of threads to use.}
43
-
44
- \item{verbosity}{Verbosity. Use 0 to run quietly, increase for additional information.}
45
-
46
- \item{points}{Optional. If passed, the MDS step is skipped and this object is used
47
- instead. It can be the \code{$points} slot of class \code{metaMDS}
48
- (from \code{vegan}).
49
- It must be a matrix or matrix-coercible object, with samples as rows and
50
- dimensions as columns.}
51
-
52
- \item{pre.tribs}{Optional. If passed, the points are recovered from this object (except if
53
- \code{points} is also passed. This should be an \code{\link{enve.TRIBS}} object
54
- estimated on the same objects (the selection is unimportant).}
55
- }
56
- \value{
57
- Returns an \code{\link{enve.TRIBS}} object.
58
- }
59
- \description{
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- Subsample any objects in "distance space" to reduce the effect of
61
- sample-clustering. This function was originally designed to subsample
62
- genomes in "phylogenetic distance space", a clear case of strong
63
- clustering bias in sampling, by Luis M. Rodriguez-R and Michael R
64
- Weigand.
65
- }
66
- \author{
67
- Luis M. Rodriguez-R [aut, cre]
68
- }
@@ -1,28 +0,0 @@
1
- % Generated by roxygen2: do not edit by hand
2
- % Please edit documentation in R/tribs.R
3
- \name{enve.tribs.test}
4
- \alias{enve.tribs.test}
5
- \title{Enveomics: TRIBS Test}
6
- \usage{
7
- enve.tribs.test(dist, selection, bins = 50, ...)
8
- }
9
- \arguments{
10
- \item{dist}{Distances as \code{dist} object.}
11
-
12
- \item{selection}{Selection defining the subset.}
13
-
14
- \item{bins}{Number of bins to evaluate in the range of distances.}
15
-
16
- \item{...}{Any other parameters supported by \code{\link{enve.tribs}},
17
- except \code{subsamples}.}
18
- }
19
- \value{
20
- Returns an \code{\link{enve.TRIBStest}} object.
21
- }
22
- \description{
23
- Estimates the empirical difference between all the distances in a set of
24
- objects and a subset, together with its statistical significance.
25
- }
26
- \author{
27
- Luis M. Rodriguez-R [aut, cre]
28
- }
@@ -1,27 +0,0 @@
1
- % Generated by roxygen2: do not edit by hand
2
- % Please edit documentation in R/utils.R
3
- \name{enve.truncate}
4
- \alias{enve.truncate}
5
- \title{Enveomics: Truncate}
6
- \usage{
7
- enve.truncate(x, f = 0.95, FUN = mean)
8
- }
9
- \arguments{
10
- \item{x}{A vector of numbers.}
11
-
12
- \item{f}{The fraction of values to retain.}
13
-
14
- \item{FUN}{Summary function to apply to the vectors. To obtain the
15
- truncated vector itself, use \code{c}.}
16
- }
17
- \value{
18
- Returns the summary \code{(FUN)} of the truncated vector.
19
- }
20
- \description{
21
- Removes the \code{n} highest and lowest values from a vector, and applies
22
- summary function. The value of \code{n} is determined such that the central
23
- range is used, corresponding to the \code{f} fraction of values.
24
- }
25
- \author{
26
- Luis M. Rodriguez-R [aut, cre]
27
- }
@@ -1,14 +0,0 @@
1
-
2
- \name{growth.curves}
3
- \docType{data}
4
- \alias{growth.curves}
5
- \title{Bacterial growth curves for three Escherichia coli mutants}
6
- \description{
7
- This data set provides time (first column) and three triplicated growth
8
- curves as optical density at 600nm (OD_600nm) for different mutants of E.
9
- coli.
10
- }
11
- \usage{growth.curves}
12
- \format{A data frame with 16 rows (times) and 10 rows (times and OD_600nm).}
13
- \keyword{datasets}
14
-