Supported by Dr. Osamu Ogasawara and  providing  . |
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Last data update: 2014.03.03 |
Public CGH data of VeltmanDescriptionThe data consist of 2 bladder cancer tumors obtained by Veltman et al (2003). Usagedata(veltman) Sourcehttp://cancerres.aacrjournals.org/cgi/content/full/63/11/2872 ReferencesJoris A. Veltman, Jane Fridlyand, Sunanda Pejavar, Adam B. Olshen, James E. Korkola, Sandy DeVries, Peter Carroll, Wen-Lin Kuo, Daniel Pinkel, Donna Albertson, Carlos Cordon-Cardo, Ajay N. Jain and Frederic M. Waldman. Array-based Comparative Genomic Hybridization for Genome-Wide Screening of DNA Copy Number in Bladder Tumors. Cancer Research 63, 2872-2880, 2003. Examplesdata(veltman) P9 Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)
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> library(GLAD)
######################################################################################
Have fun with GLAD
For smoothing it is possible to use either
the AWS algorithm (Polzehl and Spokoiny, 2002,
or the HaarSeg algorithm (Ben-Yaacov and Eldar, Bioinformatics, 2008,
If you use the package with AWS, please cite:
Hupe et al. (Bioinformatics, 2004, and Polzehl and Spokoiny (2002,
If you use the package with HaarSeg, please cite:
Hupe et al. (Bioinformatics, 2004, and (Ben-Yaacov and Eldar, Bioinformatics, 2008,
For fast computation it is recommanded to use
the daglad function with smoothfunc=haarseg
######################################################################################
New options are available in daglad: see help for details.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GLAD/veltman.Rd_%03d_medium.png", width=480, height=480)
> ### Name: veltman
> ### Title: Public CGH data of Veltman
> ### Aliases: P9 P20
> ### Keywords: datasets
>
> ### ** Examples
>
> data(veltman)
> P9
Clone Chromosome Array gene LogRatio PosOrder
1 RP11-82d16 1 Array1 -0.08723 1
2 RP11-62m23 1 Array1 -0.17480 2
3 RP11-60j11 1 Array1 -0.14258 3
4 RP11-111O05 1 Array1 -0.04524 4
5 BAL01B2579 1 Array2 D1S1612-A -0.02598 5
6 RP11-51b04 1 Array1 -0.31793 6
7 RP11-199o01 1 Array1 -0.01194 7
8 RP11-188f07 1 Array1 -0.08723 8
9 RP11-178m15 1 Array1 -0.11148 9
10 RP11-265f14 1 Array1 -0.04524 10
11 RP11-219f04 1 Array1 -0.05489 11
12 RP11-145c04 1 Array1 -0.15160 12
13 BAL01B2584 1 Array2 D1S552-A -0.20448 13
14 RP11-224f08 1 Array1 -0.21839 14
15 CIT01B2513 1 Array2 EPHB2 -0.21717 15
16 RP11-72i19 1 Array1 -0.00598 16
17 RP11-57f20 1 Array1 -0.19414 17
18 RP11-285h13 1 Array1 -0.10592 18
19 RP11-4o06 1 Array1 -0.08157 19
20 VSRMC01P057 1 Array1 -0.21320 20
21 CIT01B2859 1 Array2 FGR -0.30024 21
22 BAL01B2598 1 Array2 D1S1622-A -0.67693 22
23 RP11-62b23 1 Array1 -0.26403 23
24 RMC01P053 1 Array2 CRTM -0.30073 24
25 CIT01B2260 1 Array2 LCK -0.08552 25
26 RP11-104j13 1 Array1 -0.24224 26
27 RP11-118e03 1 Array1 -0.20458 27
28 RP11-161a11 1 Array1 -0.05297 28
29 RP11-51a20 1 Array1 -0.14077 29
30 RP11-4p06 1 Array1 0.02825 30
31 RP11-219o07 1 Array1 -0.27398 31
32 RP11-207p05 1 Array1 -0.10220 32
33 BAL01B2585 1 Array2 D1S255-A 0.40869 33
34 RP11-192a12 1 Array1 NA 34
35 VSRMC01P52 1 Array1 -0.14439 35
36 RP11-88o02 1 Array1 NA 36
37 RP11-253m24 1 Array1 -0.07400 37
38 CIT01B2354 1 Array2 TAL1 -0.11647 38
39 RP11-235b24 1 Array1 0.05084 39
40 RP11-55m23 1 Array1 -0.03553 40
41 RP11-195g13 1 Array1 -0.16236 41
42 RP11-149k24 1 Array1 -0.02771 42
43 RP11-12l18 1 Array1 -0.05297 43
44 CIT01B2927 1 Array2 JUN -0.01954 44
45 RP11-110a23 1 Array1 -0.14439 45
46 RP11-8f24 1 Array1 0.00801 46
47 RP11-69g14 1 Array1 0.02825 47
48 RP11-30a05 1 Array1 0.03233 48
49 RP11-265c04 1 Array1 -0.11885 49
50 RP11-246n19 1 Array1 -0.10592 50
51 RP11-111n18 1 Array1 0.05706 51
52 RMC01P081 1 Array2 NOEY2 0.04813 52
53 RMC01P004 1 Array2 GADD45 -0.12207 53
54 RP11-114k16 1 Array1 0.07379 54
55 RP11-80g24 1 Array1 0.06540 55
56 RP11-198h14 1 Array1 0.04464 56
57 RP11-267m21 1 Array1 -0.09847 57
58 RP11-89a19 1 Array1 -0.04718 58
59 RP11-6b16 1 Array1 0.01003 59
60 RP11-246o04 1 Array1 0.04258 60
61 RP11-78e18 1 Array1 0.08434 61
62 RP11-254e16 1 Array1 -0.00797 62
63 RP11-211d04 1 Array1 -0.13896 63
64 RP11-125p20 1 Array1 0.08434 64
65 CIT01B2498 1 Array2 TGFBR3 0.00328 65
66 RP11-156m23 1 Array1 0.04258 66
67 RP11-156g15 1 Array1 -0.00996 67
68 RP11-182h02 1 Array1 -0.07590 68
69 RP11-178m11 1 Array1 NA 69
70 RMC01P025 1 Array2 AMY2B 0.18157 70
71 RP11-96f24 1 Array1 -0.15520 71
72 CIT01B2510 1 Array2 CSF1 -0.15355 72
73 RP11-260a24 1 Array1 -0.19414 73
74 RP11-284n08 1 Array1 -0.12803 74
75 RP11-82a16 1 Array1 -0.11517 75
76 RP11-72m14 1 Array1 -0.16592 76
77 RP11-254k01 1 Array1 -0.13532 77
78 VSNRAS_304A 1 Array1 -0.07400 78
79 RMC01B3015A 1 Array2 NRAS -0.01464 79
80 VS01B2661 1 Array2 NRAS -0.04678 80
81 RP11-130b18 1 Array1 -0.37297 81
82 RP11-192j08 1 Array1 0.03438 82
83 RP11-29m22 1 Array1 -0.09660 83
84 RP11-30i17 1 Array1 0.17844 84
85 RP11-105e14 1 Array1 -0.08535 85
86 RP11-71l20 1 Array1 -0.18889 86
87 RMC01P001 1 Array2 HSTRKR/TRK -0.29278 87
88 RP11-137m19 1 Array1 0.02825 88
89 RP11-8d14 1 Array1 -0.14077 89
90 RP11-97g24 1 Array1 -0.00797 90
91 RP11-260g23 1 Array1 0.01406 91
92 CIT01B2479 1 Array2 Hs.71891 -0.08845 92
93 CIT01B2460 1 Array2 RGS5 0.09488 93
94 RP11-193j05 1 Array1 -0.12069 94
95 RP11-234m03 1 Array1 0.09071 95
96 RP11-167m06 1 Array1 -0.03162 96
97 RP11-249c05 1 Array1 0.02825 97
98 RP11-171h24 1 Array1 -0.12620 98
99 RP11-184n12 1 Array1 -0.00399 99
100 RP11-165a08 1 Array1 0.13830 100
101 CIT01B2844 1 Array2 MYOC -0.03511 101
102 RMC01P068 1 Array2 CH1 NA 102
103 RP11-177m16 1 Array1 0.30110 103
104 RP11-137n24 1 Array1 0.03847 104
105 RP11-4j02 1 Array1 0.01607 105
106 RP11-162l13 1 Array1 0.04053 106
107 RP11-118p13 1 Array1 -0.08346 107
108 RP11-212k09 1 Array1 0.04258 108
109 VSLAMC2_296B 1 Array1 -0.01194 109
110 VS01B2664 1 Array2 LAMC2 NA 110
111 RP11-134c01 1 Array1 -0.12803 111
112 CIT01B2391 1 Array2 Hs.64754 0.21766 112
113 BAL01B2592 1 Array2 D1S1660-A 0.04508 113
114 RP11-249c10 1 Array1 -0.07968 114
115 RP11-150l07 1 Array1 -0.34964 115
116 RP11-246j15 1 Array1 -0.27233 116
117 RP11-65i22 1 Array1 -0.37142 117
118 RP11-243m13 1 Array1 -0.35901 118
119 RP11-249h15 1 Array1 -0.25066 119
120 RP11-219p13 1 Array1 -0.21667 120
121 RP11-57i17 1 Array1 -0.14800 121
122 RP11-45f21 1 Array1 -0.11517 122
123 CIT01B2871 1 Array2 CHRM3 -0.06254 123
124 RP11-167j02 1 Array1 -0.12803 124
125 RP11-104a02 1 Array1 -0.11885 125
126 RP11-123o06 1 Array1 -0.06448 126
127 RP11-216f01 1 Array1 -0.03747 127
128 RP11-193p21 1 Array1 -0.13168 128
129 RP11-74e06 1 Array1 -0.06639 129
130 RP11-124a11 1 Array1 0.05084 130
131 RP11-260a10 1 Array1 NA 131
132 CIT01B2855 1 Array2 TGFB2 -0.07504 132
133 RP11-211k12 1 Array1 0.11431 133
134 RP11-149c08 1 Array1 -0.13168 134
135 CIT01B2473 1 Array2 TP53BP2 -0.09975 135
136 RP11-192m01 1 Array1 -0.23743 136
137 RP11-210e16 1 Array1 -0.03162 137
138 RP11-155c15 1 Array1 NA 138
139 CIT01B2470 1 Array2 GNG4 -0.16846 139
140 RP11-130i13 1 Array1 0.11648 140
141 RP11-210f08 1 Array1 -0.09286 141
142 RP11-194f13 1 Array1 -0.09473 142
143 RP11-212e22 1 Array1 -0.45397 143
144 RP11-200f14 2 Array1 -0.18714 144
145 RP11-185p14 2 Array1 -0.10777 145
146 RP11-87j07 2 Array1 -0.30181 146
147 RP11-81f24 2 Array1 -0.17126 147
148 CIT02B2888 2 Array2 MYCN -0.30079 148
149 VSLSI_NMYC_B 2 Array1 -0.16414 149
150 RP11-111J06 2 Array1 -0.02771 150
151 RP11-171a13 2 Array1 -0.16057 151
152 RP11-57f09 2 Array1 -0.31311 152
153 RP11-72h12 2 Array1 -0.19763 153
154 RP11-71j07 2 Array1 -0.11885 154
155 RP11-163n23 2 Array1 -0.00200 155
156 RMC02P020 2 Array2 PKR NA 156
157 CIT02B2522 2 Array2 CBF -0.03562 157
158 RP11-163n11 2 Array1 -0.12253 158
159 RP11-128c05 2 Array1 -0.13350 159
160 RP11-119j12 2 Array1 -0.23716 160
161 RP11-180l21 2 Array1 -0.13168 161
162 CIT02B2842 2 Array2 MSH2 -0.22426 162
163 VS02B2665 2 Array2 Rel -0.19454 163
164 VSBAC_274P9_REL 2 Array1 -0.33228 164
165 CIT02B2494 2 Array2 PLEK -0.11491 165
166 RP11-24p23 2 Array1 -0.29368 166
167 RP11-87c16 2 Array1 -0.17303 167
168 CIT02B2442 2 Array2 TACR1 -0.13896 168
169 RP11-63d13 2 Array1 -0.05297 169
170 RP11-113n17 2 Array1 -0.19589 170
171 RP11-84m16 2 Array1 0.31595 171
172 RP11-82b19 2 Array1 0.10784 172
173 RP11-67l23 2 Array1 -0.12069 173
174 RMC02P002 2 Array2 ZAP70 -0.31797 174
175 RP11-8c18 2 Array1 -0.23036 175
176 RP11-95h05 2 Array1 -0.09098 176
177 RP11-218f21 2 Array1 -0.14980 177
178 RP11-9l19 2 Array1 -0.19763 178
179 RP11-1l22 2 Array1 -0.16502 179
180 RP11-29n17 2 Array1 -0.08723 180
181 RP11-119N03 2 Array1 -0.02771 181
182 RP11-72h23 2 Array1 -0.10220 182
183 BAL02B2599 2 Array2 D2S1399-A -0.12101 183
184 CIT02B2476 2 Array2 ARHE -0.06099 184
185 RMC02B3369A 2 Array2 RND3 -0.05125 185
186 RP11-13c20 2 Array1 -0.20542 186
187 RP11-185m22 2 Array1 -0.01590 187
188 RP11-191i09 2 Array1 0.02126 188
189 CIT02B2506 2 Array2 ACVR1 -0.07194 189
190 RP11-50j20 2 Array1 -0.04718 190
191 RP11-39a08 2 Array1 0.16263 191
192 RP11-218d15 2 Array1 -0.18538 192
193 RP11-61n23 2 Array1 NA 193
194 RP11-12n07 2 Array1 0.57104 194
195 RP11-38i11 2 Array1 0.37951 195
196 RP11-69g04 2 Array1 0.38211 196
197 RP11-30m01 2 Array1 0.46453 197
198 RP11-34n13 2 Array1 NA 198
199 RP11-57C06 2 Array1 0.41105 199
200 RP11-225l15 2 Array1 0.20584 200
201 CIT02B2830 2 Array2 ERBB4 -1.05044 201
202 RP11-4b06 2 Array1 NA 202
203 RP11-53g06 2 Array1 -1.06352 203
204 RP11-183n07 2 Array1 -0.88461 204
205 RP11-68h19 2 Array1 -0.83842 205
206 RP11-71h20 2 Array1 -1.00499 206
207 RP11-188b21 2 Array1 -1.17657 207
208 CIT02B2512 2 Array2 INPP5D -1.27663 208
209 RP11-21k01 2 Array1 -1.10220 209
210 RP11-116m19 2 Array1 -1.07400 210
211 VSTERC_300B 3 Array1 0.06123 211
212 RP11-32f23 3 Array1 0.12299 212
213 RP11-121D03 3 Array1 0.30603 213
214 RP11-28p14 3 Array1 0.24083 214
215 SAT03A2205.c6 3 Array2 D3S3591 0.17591 215
216 RP11-128a05 3 Array1 NA 216
217 RMC03P052 3 Array2 VHL NA 217
218 RP11-175G07 3 Array1 0.12953 218
219 VSBAC_98L2_RAF1 3 Array1 0.11864 219
220 CIT03B2556 3 Array2 RAF1 0.07746 220
221 VS03B2667 3 Array2 RAF1 0.01155 221
222 RP11-271e02 3 Array1 -0.02771 222
223 RMC03P002 3 Array2 HSTAURN -0.05564 223
224 RP11-279l16 3 Array1 NA 224
225 RP11-255o19 3 Array1 -0.03162 225
226 RP11-208g16 3 Array1 0.15156 226
227 RP11-245E05 3 Array1 0.04671 227
228 RP11-41f05 3 Array1 0.11431 228
229 RP11-03B2720 3 Array2 D3S3598 0.03653 229
230 RMC03B3420B 3 Array2 THRB 0.15392 230
231 RMC03P060 3 Array2 RARB 0.20803 231
232 RP11-11L06 3 Array1 0.19207 232
233 RP11-103n21 3 Array1 0.31595 233
234 RP11-286g05 3 Array1 0.11648 234
235 CIT03B2890 3 Array2 PLCD1 NA 235
236 RP11-209O16 3 Array1 0.14050 236
237 RG03A2215.c2 3 Array2 D3S4063 0.12672 237
238 RP11-119l02 3 Array1 0.08434 238
239 RP11-03B2721 3 Array2 D3S3564 0.04665 239
240 SAT03A2223.c6 3 Array2 SGC30603 0.13751 240
241 RP11-189H19 3 Array1 0.21508 241
242 RP11-111p21 3 Array1 0.06331 242
243 RMC03B2079A 3 Array2 CDC25A NA 243
244 RG03A2225 3 Array2 RhoA -0.03081 244
245 CIT03B2930 3 Array2 LUCA15 -0.02233 245
246 RMC03P049 3 Array2 TKT -0.17136 246
247 CIT03B2909 3 Array2 CAC1D -0.03881 247
248 RP11-122d19 3 Array1 NA 248
249 RP11-124o02 3 Array1 0.14713 249
250 RP11-120C02 3 Array1 0.17167 250
251 RP11-229a12 3 Array1 0.06540 251
252 RP11-169g24 3 Array1 NA 252
253 RP11-180G14 3 Array1 0.15378 253
254 RP11-39L01 3 Array1 -0.02378 254
255 RP11-94d19 3 Array1 0.22439 255
256 CIT03B2874 3 Array2 FHIT 0.10735 256
257 RP11-114p15 3 Array1 NA 257
258 RP11-129B22 3 Array1 0.20814 258
259 RP11-03B2722 3 Array2 D3S1287 0.09311 259
260 RP11-179B09 3 Array1 0.10569 260
261 CIT03B2959 3 Array2 Hs.7910 0.02982 261
262 CIT03B2962 3 Array2 DOC1 0.12315 262
263 RP03B2724 3 Array2 D3S1271 0.12782 263
264 RP11-03B2724 3 Array2 D3S1271 0.05008 264
265 RP11-69n24 3 Array1 0.09925 265
266 RP11-129p02 3 Array1 0.07800 266
267 RP11-166c10 3 Array1 0.12299 267
268 RP11-12p11 3 Array1 0.22206 268
269 RP03B2725 3 Array2 D3S1572 0.12854 269
270 RP11-03B2725 3 Array2 D3S1572 0.16344 270
271 RP11-153k19 3 Array1 -0.23716 271
272 RP11-5k13 3 Array1 0.04053 272
273 RMC03P043 3 Array2 DRD3 0.23061 273
274 RP11-214a05 3 Array1 0.05084 274
275 RP11-233l03 3 Array1 0.22907 275
276 RP11-165b13 3 Array1 0.05499 276
277 RP03B2726 3 Array2 D3S1303 0.14658 277
278 RP11-03B2726 3 Array2 D3S1303 NA 278
279 RP11-169n13 3 Array1 0.06540 279
280 RP11-95h16 3 Array1 0.26224 280
281 CIT03B2452 3 Array2 Rho 0.00328 281
282 RP11-59j16 3 Array1 -0.02967 282
283 RP11-205a06 3 Array1 NA 283
284 RP03B2727 3 Array2 D3S1589 0.06368 284
285 RMC03P047 3 Array2 ZNF9 -0.06099 285
286 RMC03B3424A 3 Array2 D3S3514 0.11263 286
287 RMC03B3424B 3 Array2 D3S3514 0.34722 287
288 RP11-220j13 3 Array1 0.14271 288
289 RP11-219p10 3 Array1 0.13391 289
290 RJ03B2749B 3 Array2 D3S3528 0.16876 290
291 RJ03B2751B 3 Array2 D3S3528 -0.02713 291
292 RMC03B3413B 3 Array2 D3S3528 0.14656 292
293 RP11-162j10 3 Array1 -0.04524 293
294 RP03B2728 3 Array2 D3S1576 0.16177 294
295 RP11-03B2728 3 Array2 D3S1576 0.27983 295
296 RP11-3B2728 3 Array2 D3S1576 0.10365 296
297 RMC03B3388A 3 Array2 P110B 0.11426 297
298 RP11-166d18 3 Array1 0.02621 298
299 RP11-160a13 3 Array1 NA 299
300 RMC03P068 3 Array2 I-plas 0.18519 300
301 RP11-165m11 3 Array1 0.10999 301
302 RP03B2729 3 Array2 D3S1557 0.01981 302
303 RP11-72e23 3 Array1 0.30603 303
304 CIT03B2515 3 Array2 AGTR 0.26566 304
305 RP11-229g06 3 Array1 0.42171 305
306 RP11-145f16 3 Array1 0.01810 306
307 RP11-64f06 3 Array1 0.07169 307
308 RP11-65l11 3 Array1 0.08646 308
309 RP11-03B2730 3 Array2 D3S1280 NA 309
310 RP11-209h21 3 Array1 0.02825 310
311 RP03B2731 3 Array2 D3S1553 0.22531 311
312 RP03B2732 3 Array2 D3S3579 0.11283 312
313 RP11-03B2732 3 Array2 D3S3579 0.22124 313
314 RP11-03B2733 3 Array2 D3S1268 NA 314
315 RP11-198g24 3 Array1 0.27911 315
316 RP03B2734 3 Array2 D3S3673 0.15565 316
317 RP11-3B2734 3 Array2 D3S3673 0.17962 317
318 RP03B2736 3 Array2 D3S1282 0.05753 318
319 RP03B2735 3 Array2 D3S1614 0.28559 319
320 RP11-24l16 3 Array1 0.10354 320
321 RMC03B3431B 3 Array2 EVI1 0.25000 321
322 VS03B2668 3 Array2 hTR/TERC 0.08460 322
323 RP11-141c22 3 Array1 0.18979 323
324 NIH B2977 3 Array2 WI-14970 0.17405 324
325 NIH03 B2980 3 Array2 D3S1246 0.09493 325
326 NIH03B2988 3 Array2 GLUT-2 0.26763 326
327 RMC03P008 3 Array2 Glut2 0.13067 327
328 RP11-163h06 3 Array1 0.21045 328
329 RP03B2737 3 Array2 D3S3725 0.10929 329
330 RP11-03B2737 3 Array2 D3S3725 0.25584 330
331 RP03B2738 3 Array2 D3S3520 0.17224 331
332 RP11-03B2738 3 Array2 D3S3520 0.33642 332
333 RP11-3B2738 3 Array2 D3S3520 0.20393 333
334 RP11-196f13 3 Array1 0.14713 334
335 RP11-172g05 3 Array1 0.32093 335
336 RP03B2739 3 Array2 D3S1548 0.24806 336
337 RP11-148d23 3 Array1 0.16046 337
338 RP03B2740 3 Array2 D3S1565 NA 338
339 RP03B2741 3 Array2 D3S3715 0.12494 339
340 RP11-03B2741 3 Array2 D3S3715 0.29755 340
341 VSLSI_PIK3CA_210D 3 Array1 0.10569 341
342 RG03B22240 3 Array2 PIK3CA 0.00000 342
343 RG03B2237 3 Array2 PIK3CA 0.07578 343
344 RMC03B3338A 3 Array2 PIK3CA 0.07578 344
345 RP03B2742 3 Array2 D3S3565 0.02985 345
346 RP11-118f04 3 Array1 -0.06829 346
347 CIT03B2399 3 Array2 THPO -0.26966 347
348 RMC03P051 3 Array2 SST 0.04835 348
349 RMC03P061 3 Array2 BCL6 0.04667 349
350 RP11-67e18 3 Array1 0.25030 350
351 RP11-178k17 3 Array1 NA 351
352 RP03B2743 3 Array2 D3S1294 0.14166 352
353 RP11-03B2743 3 Array2 D3S1294 0.16069 353
354 RP11-3B2744 3 Array2 D3S1314 0.23862 354
355 RP11-3B2745 3 Array2 D3S1601 0.28171 355
356 RMC03P048 3 Array2 TFRC 0.21912 356
357 RP11-3B2746 3 Array2 D3S1272 0.08099 357
358 RP11-233n20 3 Array1 -0.02771 358
359 RP11-69L07 4 Array1 0.05914 359
360 RP11-20i20 4 Array1 -0.05297 360
361 RMC04P002 4 Array2 GPRKLG -0.05938 361
362 RP11-237C24 4 Array1 0.11648 362
363 RP11-7a06 4 Array1 NA 363
364 RP11-97h19 4 Array1 NA 364
365 RP11-101J14 4 Array1 -0.06829 365
366 RP11-17i09 4 Array1 -0.01590 366
367 RP11-34C20 4 Array1 0.05084
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Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and