Supported by Dr. Osamu Ogasawara and  providing  . |
|
Last data update: 2014.03.03 |
Sampling Site Short NamesDescriptionCharacter vector with the names of the sampling sites, corresponding to
the names used to denote amplicon frequencies in
the Usagedata(site.f) FormatThe format is: chr [1:8] "FU25" "FU28" "FU31.1" "FU31.2" "FU34" "FU37" "UniPond" "BogSoil" ReferencesBoenigk J, Heider D, Jost S, Lange A, Budeus B, Schilling E, Strittmatter A, Hoffmann D: A high-throughput amplicon sequencing and analysis protocol for comparative analyses of microbial communities (submitted) Examplesdata(site.f) data(ampliconfreqs) ampliconduo(ampliconfreqs[,1:6], sample.names = site.f[1:3]) Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(AmpliconDuo)
Loading required package: ggplot2
Loading required package: xtable
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/AmpliconDuo/site.f.Rd_%03d_medium.png", width=480, height=480)
> ### Name: site.f
> ### Title: Sampling Site Short Names
> ### Aliases: site.f
> ### Keywords: datasets
>
> ### ** Examples
>
> data(site.f)
> data(ampliconfreqs)
> ampliconduo(ampliconfreqs[,1:6], sample.names = site.f[1:3])
...$FU25
freqA freqB p OR CI.low CI.up
2 0 1912 0.000000e+00 0.00000000 0.000000e+00 2.223048e-03
7 0 1628 0.000000e+00 0.00000000 0.000000e+00 2.628342e-03
8 1 1 1.000000e+00 1.19462627 1.522582e-02 9.371064e+01
9 747 903 8.229476e-01 0.98810568 8.950905e-01 1.090548e+00
10 670 0 2.784538e-230 Inf 2.173001e+02 Inf
11 1120 0 0.000000e+00 Inf 3.700044e+02 Inf
13 0 613 4.171228e-163 0.00000000 0.000000e+00 7.181744e-03
14 7 3 2.021179e-01 2.78764357 6.363627e-01 1.670618e+01
15 1075 1281 9.501087e-01 1.00256122 9.229650e-01 1.088869e+00
17 1646 1987 7.612681e-01 0.98933266 9.253611e-01 1.057587e+00
19 787 0 1.527275e-270 Inf 2.569913e+02 Inf
20 1096 1392 1.277021e-01 0.93953299 8.666225e-01 1.018428e+00
22 545 616 3.439255e-01 1.05739719 9.401198e-01 1.189157e+00
23 1014 679 1.379731e-32 1.79678858 1.627793e+00 1.984332e+00
25 504 550 1.445820e-01 1.09547437 9.683503e-01 1.239068e+00
30 335 568 2.747849e-07 0.70300555 6.121104e-01 8.063989e-01
31 783 951 7.341738e-01 0.98338225 8.929571e-01 1.082742e+00
32 821 768 9.880680e-07 1.28071048 1.158607e+00 1.415804e+00
34 475 533 3.252594e-01 1.06509487 9.388082e-01 1.208204e+00
35 715 736 4.569640e-03 1.16237740 1.046646e+00 1.290849e+00
36 603 920 2.441169e-06 0.78091068 7.031349e-01 8.668015e-01
37 299 363 8.450409e-01 0.98392758 8.411174e-01 1.150270e+00
38 2 1 5.949510e-01 2.38929608 1.243747e-01 1.408484e+02
39 535 667 4.672625e-01 0.95784500 8.528286e-01 1.075431e+00
40 647 599 7.080045e-06 1.29335380 1.154930e+00 1.448511e+00
43 0 434 1.615077e-115 0.00000000 0.000000e+00 1.011920e-02
44 459 0 8.325554e-158 Inf 1.493513e+02 Inf
45 784 810 3.624606e-03 1.15824345 1.047963e+00 1.280091e+00
49 519 769 1.310701e-04 0.80465363 7.181275e-01 9.010732e-01
50 0 677 4.558512e-180 0.00000000 0.000000e+00 6.455672e-03
51 840 769 9.058828e-08 1.30902550 1.184931e+00 1.446261e+00
52 641 590 4.741029e-06 1.30093715 1.160888e+00 1.458132e+00
53 0 3 2.558932e-01 0.00000000 0.000000e+00 2.891023e+00
55 0 350 2.577026e-93 0.00000000 0.000000e+00 1.257067e-02
56 608 502 7.375551e-10 1.45120603 1.286676e+00 1.637365e+00
57 202 242 1.000000e+00 0.99715963 8.228813e-01 1.207332e+00
60 623 538 2.971931e-08 1.38717519 1.233449e+00 1.560486e+00
61 364 391 1.529937e-01 1.11278287 9.616912e-01 1.287370e+00
62 372 383 4.382627e-02 1.16126421 1.003712e+00 1.343476e+00
63 680 660 1.412200e-04 1.23333504 1.105839e+00 1.375581e+00
64 577 503 2.087780e-07 1.37377959 1.216249e+00 1.552105e+00
65 225 270 9.639853e-01 0.99550717 8.300735e-01 1.193027e+00
66 531 617 6.553892e-01 1.02836305 9.135221e-01 1.157323e+00
67 774 905 6.751777e-01 1.02197860 9.267299e-01 1.126819e+00
68 637 563 1.793172e-07 1.35521851 1.207454e+00 1.521390e+00
70 610 521 1.629181e-08 1.40257376 1.245147e+00 1.580346e+00
71 447 466 4.194338e-02 1.14695746 1.004664e+00 1.309238e+00
72 217 297 1.315072e-01 0.87241034 7.286494e-01 1.043165e+00
75 626 546 6.716247e-08 1.37335206 1.221843e+00 1.543970e+00
76 312 384 7.029883e-01 0.97048555 8.327984e-01 1.130236e+00
77 1012 1313 4.838179e-02 0.91944752 8.456873e-01 9.995067e-01
79 488 582 1.000000e+00 1.00169424 8.858944e-01 1.132241e+00
80 703 654 4.089134e-06 1.28732314 1.155022e+00 1.434910e+00
85 448 652 1.265961e-03 0.81957023 7.247228e-01 9.261893e-01
86 364 168 2.599115e-26 2.59756072 2.157038e+00 3.138520e+00
88 90 106 9.428559e-01 1.01432940 7.571160e-01 1.356474e+00
90 1659 1526 9.833809e-14 1.30679697 1.217292e+00 1.402970e+00
92 0 6 3.496213e-02 0.00000000 0.000000e+00 1.014579e+00
94 567 493 2.233997e-07 1.37731688 1.217967e+00 1.557920e+00
95 552 765 7.606602e-03 0.86079027 7.697454e-01 9.621289e-01
97 709 629 5.244095e-08 1.35049032 1.210667e+00 1.506769e+00
98 0 37 1.786095e-10 0.00000000 0.000000e+00 1.252080e-01
99 1 1 1.000000e+00 1.19462627 1.522582e-02 9.371064e+01
100 41 40 3.737974e-01 1.22463334 7.725057e-01 1.942675e+00
101 267 305 6.137666e-01 1.04600589 8.838920e-01 1.237243e+00
105 347 421 8.558834e-01 0.98455992 8.513197e-01 1.138047e+00
108 473 489 2.500226e-02 1.15671065 1.016736e+00 1.315851e+00
109 396 0 3.367969e-136 Inf 1.281563e+02 Inf
110 494 490 3.461263e-03 1.20598629 1.061661e+00 1.369955e+00
111 891 1134 1.568204e-01 0.93774166 8.574514e-01 1.025342e+00
112 378 456 9.166951e-01 0.99022474 8.613292e-01 1.137878e+00
113 554 806 3.353281e-04 0.81953985 7.338186e-01 9.147696e-01
115 392 424 1.585978e-01 1.10511839 9.604329e-01 1.271357e+00
116 320 467 5.698507e-03 0.81766646 7.067684e-01 9.450597e-01
117 1218 1436 7.380143e-01 1.01353383 9.375505e-01 1.095537e+00
118 226 332 1.702450e-02 0.81254147 6.828962e-01 9.653935e-01
121 178 208 8.379468e-01 1.02239445 8.319696e-01 1.255305e+00
122 259 313 8.996513e-01 0.98847814 8.348494e-01 1.169550e+00
123 879 1082 5.079791e-01 0.97007665 8.858975e-01 1.062057e+00
124 171 204 1.000000e+00 1.00138302 8.121756e-01 1.233451e+00
126 552 575 2.244093e-02 1.14813498 1.019217e+00 1.293260e+00
128 338 431 3.836190e-01 0.93649810 8.094619e-01 1.082801e+00
130 552 646 7.267157e-01 1.02098490 9.092136e-01 1.146165e+00
131 573 402 1.288346e-16 1.70919708 1.501274e+00 1.947347e+00
133 284 374 2.239440e-01 0.90675954 7.740622e-01 1.061212e+00
134 294 0 3.007953e-101 Inf 9.499032e+01 Inf
136 9 24 3.656820e-02 0.44791981 1.832091e-01 9.982118e-01
137 547 716 1.119700e-01 0.91186249 8.139183e-01 1.021206e+00
139 384 424 2.721760e-01 1.08242369 9.399853e-01 1.246164e+00
140 20 35 1.784801e-01 0.68254729 3.733192e-01 1.215646e+00
141 27 0 6.052592e-10 Inf 8.162108e+00 Inf
142 2 0 2.076225e-01 Inf 2.243624e-01 Inf
144 481 634 1.031536e-01 0.90564286 8.023592e-01 1.021680e+00
146 0 203 2.244592e-54 0.00000000 0.000000e+00 2.182713e-02
147 492 665 3.799092e-02 0.88294550 7.837883e-01 9.940802e-01
148 231 253 3.605779e-01 1.09107924 9.085789e-01 1.309734e+00
151 1 0 4.556581e-01 Inf 3.063118e-02 Inf
152 0 137 1.013698e-36 0.00000000 0.000000e+00 3.254633e-02
154 361 474 1.853903e-01 0.90934404 7.904177e-01 1.045378e+00
158 307 431 3.156851e-02 0.85020292 7.317367e-01 9.869021e-01
159 64 81 7.395303e-01 0.94383370 6.690941e-01 1.326579e+00
163 0 111 8.620155e-30 0.00000000 0.000000e+00 4.031283e-02
165 388 513 1.311788e-01 0.90296877 7.889910e-01 1.032677e+00
167 0 227 9.968064e-61 0.00000000 0.000000e+00 1.953239e-02
170 239 0 2.032662e-82 Inf 7.724486e+01 Inf
171 277 380 8.401669e-02 0.87025625 7.424221e-01 1.019079e+00
172 243 333 1.111019e-01 0.87126542 7.351622e-01 1.031385e+00
173 91 96 4.192340e-01 1.13259648 8.406105e-01 1.525090e+00
174 128 159 7.669332e-01 0.96162897 7.557677e-01 1.221681e+00
176 2 0 2.076225e-01 Inf 2.243624e-01 Inf
178 0 45 1.927329e-12 0.00000000 0.000000e+00 1.020125e-01
179 2 14 9.805555e-03 0.17063767 1.883127e-02 7.429990e-01
180 165 169 1.691079e-01 1.16678498 9.355094e-01 1.455007e+00
181 0 261 1.296384e-69 0.00000000 0.000000e+00 1.694493e-02
184 77 84 5.800737e-01 1.09519038 7.931487e-01 1.510435e+00
186 301 336 4.025307e-01 1.07050383 9.128767e-01 1.254909e+00
187 131 151 7.651594e-01 1.03648906 8.136553e-01 1.318864e+00
188 112 139 7.998285e-01 0.96250538 7.434692e-01 1.243777e+00
189 1 104 2.271638e-26 0.01147129 2.930292e-04 6.533705e-02
192 48 67 4.539782e-01 0.85574449 5.779929e-01 1.258520e+00
194 65 61 1.803781e-01 1.27323679 8.837136e-01 1.836608e+00
195 0 474 5.462525e-126 0.00000000 0.000000e+00 9.282097e-03
196 196 555 4.538292e-28 0.42010127 3.549917e-01 4.954329e-01
198 178 205 7.195180e-01 1.03740714 8.436384e-01 1.274665e+00
200 2 0 2.076225e-01 Inf 2.243624e-01 Inf
202 31 32 6.134669e-01 1.15736987 6.829686e-01 1.958945e+00
206 0 1 1.000000e+00 0.00000000 0.000000e+00 4.655732e+01
207 3 0 9.460326e-02 Inf 4.936873e-01 Inf
209 206 213 1.408078e-01 1.15587325 9.494477e-01 1.406991e+00
210 27 18 7.124612e-02 1.79224981 9.514015e-01 3.455385e+00
211 101 102 2.315773e-01 1.18320470 8.894449e-01 1.573832e+00
212 59 90 1.616786e-01 0.78294439 5.539093e-01 1.099463e+00
213 787 909 4.922507e-01 1.03473882 9.387801e-01 1.140320e+00
218 9 38 1.979811e-04 0.28284651 1.202424e-01 5.951777e-01
219 108 135 7.475011e-01 0.95561812 7.348329e-01 1.240287e+00
220 53 69 6.506130e-01 0.91751756 6.289515e-01 1.331968e+00
221 66 56 6.855412e-02 1.40836498 9.712924e-01 2.048498e+00
222 68 61 1.114783e-01 1.33206205 9.286666e-01 1.914280e+00
223 0 469 7.184589e-125 0.00000000 0.000000e+00 9.386070e-03
224 284 345 8.411198e-01 0.98332765 8.371317e-01 1.154343e+00
225 17 14 3.677413e-01 1.45072251 6.729703e-01 3.179417e+00
226 3 4 1.000000e+00 0.89598829 1.312192e-01 5.296571e+00
227 90 126 2.740401e-01 0.85309761 6.434302e-01 1.127239e+00
228 0 457 1.318112e-121 0.00000000 0.000000e+00 9.650968e-03
229 58 66 7.875354e-01 1.04989640 7.247291e-01 1.517316e+00
232 79 97 8.798412e-01 0.97290731 7.134461e-01 1.323331e+00
233 5 394 9.501120e-96 0.01508243 4.865684e-03 3.550355e-02
234 13 9 2.842526e-01 1.72569376 6.823830e-01 4.574179e+00
235 1 0 4.556581e-01 Inf 3.063118e-02 Inf
237 1 1 1.000000e+00 1.19462627 1.522582e-02 9.371064e+01
238 440 476 1.342902e-01 1.10500812 9.680342e-01 1.261156e+00
239 0 23 1.240506e-06 0.00000000 0.000000e+00 2.077894e-01
240 1 0 4.556581e-01 Inf 3.063118e-02 Inf
241 0 1 1.000000e+00 0.00000000 0.000000e+00 4.655732e+01
242 3 1 3.368914e-01 3.58397423 2.877458e-01 1.879691e+02
243 58 78 5.467443e-01 0.88822760 6.210417e-01 1.264014e+00
245 211 243 7.059310e-01 1.03745085 8.583109e-01 1.253094e+00
246 0 117 1.663173e-31 0.00000000 0.000000e+00 3.821340e-02
249 0 299 8.560618e-80 0.00000000 0.000000e+00 1.477112e-02
251 18 23 8.764186e-01 0.93489070 4.753926e-01 1.810895e+00
252 102 135 4.728560e-01 0.90247631 6.907046e-01 1.176038e+00
253 21 34 2.823981e-01 0.73777399 4.068595e-01 1.308486e+00
254 145 205 1.323389e-01 0.84462537 6.778701e-01 1.050195e+00
258 158 229 6.569145e-02 0.82380191 6.681241e-01 1.013616e+00
259 32 37 9.043224e-01 1.03322047 6.230343e-01 1.704906e+00
260 82 87 4.409642e-01 1.12613282 8.224252e-01 1.540846e+00
264 126 140 5.793661e-01 1.07530117 8.383125e-01 1.378135e+00
266 82 93 7.615116e-01 1.05342686 7.729765e-01 1.433334e+00
269 46 46 4.038869e-01 1.19476507 7.763244e-01 1.838720e+00
270 151 158 2.530040e-01 1.14203840 9.073835e-01 1.436923e+00
272 29 31 6.985176e-01 1.11760729 6.497896e-01 1.917125e+00
273 0 1 1.000000e+00 0.00000000 0.000000e+00 4.655732e+01
275 2 0 2.076225e-01 Inf 2.243624e-01 Inf
286 2 1 5.949510e-01 2.38929608 1.243747e-01 1.408484e+02
289 427 376 1.654558e-05 1.35907997 1.179910e+00 1.566036e+00
292 35 42 1.000000e+00 0.99552070 6.169686e-01 1.597403e+00
294 529 500 1.824176e-04 1.26613771 1.117794e+00 1.434330e+00
303 61 46 1.955854e-02 1.58472068 1.062970e+00 2.377053e+00
306 3 0 9.460326e-02 Inf 4.936873e-01 Inf
307 0 1 1.000000e+00 0.00000000 0.000000e+00 4.655732e+01
308 317 427 1.045722e-01 0.88632292 7.637091e-01 1.027760e+00
311 2 2 1.000000e+00 1.19462936 8.661430e-02 1.647725e+01
315 159 171 3.472315e-01 1.11107238 8.893710e-01 1.387398e+00
316 5 5 1.000000e+00 1.19463860 2.749193e-01 5.190983e+00
317 124 122 1.404647e-01 1.21462782 9.381046e-01 1.572890e+00
320 30 272 3.265748e-41 0.13135336 8.690479e-02 1.919355e-01
323 30 40 7.192293e-01 0.89594370 5.388195e-01 1.475120e+00
328 0 1 1.000000e+00 0.00000000 0.000000e+00 4.655732e+01
329 0 11 1.418646e-03 0.00000000 0.000000e+00 4.759288e-01
331 6 8 1.000000e+00 0.89598334 2.562219e-01 2.944771e+00
332 0 26 1.780728e-07 0.00000000 0.000000e+00 1.820510e-01
335 2 10 7.758230e-02 0.23890808 2.544991e-02 1.121117e+00
339 239 254 2.046669e-01 1.12454838 9.382089e-01 1.347529e+00
348 49 55 7.683303e-01 1.06432774 7.090540e-01 1.593644e+00
350 29 49 1.411148e-01 0.70689317 4.305432e-01 1.141613e+00
352 3 2 6.651112e-01 1.79194869 2.052650e-01 2.145096e+01
355 36 57 2.113827e-01 0.75436438 4.826900e-01 1.165144e+00
359 55 58 5.100718e-01 1.13295028 7.688545e-01 1.667686e+00
360 9 10 1.000000e+00 1.07516130 3.865291e-01 2.944389e+00
361 39 39 4.953228e-01 1.19474347 7.464659e-01 1.912237e+00
362 76 100 5.453091e-01 0.90783566 6.645287e-01 1.235873e+00
364 1 1 1.000000e+00 1.19462627 1.522582e-02 9.371064e+01
365 55 49 1.403123e-01 1.34119364 8.957639e-01 2.013229e+00
366 102 132 5.550781e-01 0.92297412 7.055751e-01 1.204532e+00
367 34 25 6.770702e-02 1.62500430 9.412758e-01 2.841490e+00
368 22 40 1.260536e-01 0.65692933 3.718241e-01 1.132362e+00
369 41 28 2.179785e-02 1.74973350 1.056101e+00 2.938268e+00
372 196 232 9.226600e-01 1.00928436 8.299623e-01 1.226302e+00
374 78 99 7.063603e-01 0.94113518 6.902332e-01 1.279435e+00
377 54 87 9.061462e-02 0.74127467 5.177232e-01 1.053079e+00
378 84 73 5.399955e-02 1.37512502 9.927414e-01 1.908709e+00
379 195 238 8.468005e-01 0.97872410 8.054796e-01 1.188113e+00
381 2 1 5.949510e-01 2.38929608 1.243747e-01 1.408484e+02
383 119 148 7.587831e-01 0.96046426 7.479364e-01 1.231280e+00
384 14 16 1.000000e+00 1.04533117 4.724704e-01 2.285882e+00
385 19 48 4.603212e-03 0.47272696 2.623765e-01 8.194399e-01
388 53 63 1.000000e+00 1.00500889 6.839164e-01 1.471862e+00
391 0 82 2.306584e-22 0.00000000 0.000000e+00 5.492128e-02
396 2 0 2.076225e-01 Inf 2.243624e-01 Inf
397 68 70 3.934248e-01 1.16066540 8.188049e-01 1.644490e+00
398 71 73 4.026733e-01 1.16207726 8.261119e-01 1.633967e+00
399 46 42 2.388243e-01 1.30861623 8.422934e-01 2.038119e+00
400 344 0 2.240689e-118 Inf 1.112588e+02 Inf
405 45 29 9.888168e-03 1.85430989 1.137350e+00 3.067255e+00
407 165 205 7.148346e-01 0.96142262 7.782333e-01 1.186284e+00
408 89 96 5.066193e-01 1.10766979 8.205371e-01 1.493898e+00
409 69 72 4.468619e-01 1.14500747 8.107853e-01 1.615982e+00
411 57 79 4.383697e-01 0.86182323 6.019285e-01 1.227220e+00
413 59 63 5.855283e-01 1.11888770 7.708428e-01 1.622108e+00
414 43 43 4.488394e-01 1.19475582 7.643238e-01 1.867624e+00
415 38 43 8.241416e-01 1.05578340 6.639723e-01 1.672763e+00
416 20 30 4.791834e-01 0.79635617 4.286012e-01 1.449605e+00
418 51 75 2.829729e-01 0.81219716 5.575178e-01 1.174879e+00
420 125 139 5.780446e-01 1.07443776 8.368204e-01 1.378439e+00
421 16 24 5.279256e-01 0.79636908 3.952554e-01 1.562721e+00
422 143 200 1.582142e-01 0.85382926 6.838285e-01 1.063850e+00
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