snpgdsHCluster: Hierarchical cluster analysis
In SNPRelate: Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data
Description
Usage
Arguments
Details
Value
Author(s)
See Also
Examples
Description
Perform hierarchical cluster analysis on the dissimilarity matrix.
Usage
1
snpgdsHCluster(dist, sample.id=NULL, need.mat=TRUE, hang=0.25)
Arguments
dist
an object of "snpgdsDissClass" from snpgdsDiss,
an object of "snpgdsIBSClass" from snpgdsIBS, or
a square matrix for dissimilarity
sample.id
to specify sample id, only work if dist is a matrix
need.mat
if TRUE, store the dissimilarity matrix in the result
hang
The fraction of the plot height by which labels should hang
below the rest of the plot. A negative value will cause the labels to
hang down from 0.
Details
Call the function hclust to perform hierarchical cluster
analysis, using method="average".
Value
Return a list (class "snpgdsHCClass"):
sample.id
the sample ids used in the analysis
hclust
an object returned from hclust
dendrogram
dist
the dissimilarity matrix, if need.mat = TRUE
Author(s)
Xiuwen Zheng
See Also
snpgdsIBS, snpgdsDiss,
snpgdsCutTree
Examples
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
# open an example dataset (HapMap)
genofile <- snpgdsOpen(snpgdsExampleFileName())
pop.group <- read.gdsn(index.gdsn(genofile, "sample.annot/pop.group"))
pop.group <- as.factor(pop.group)
pop.level <- levels(pop.group)
diss <- snpgdsDiss(genofile)
hc <- snpgdsHCluster(diss)
rv <- snpgdsCutTree(hc)
rv
# call 'plot' to draw a dendrogram
plot(rv$dendrogram, leaflab="none", main="HapMap Phase II")
# the distribution of Z scores
snpgdsDrawTree(rv, type="z-score", main="HapMap Phase II")
# draw dendrogram
snpgdsDrawTree(rv, main="HapMap Phase II",
edgePar=list(col=rgb(0.5,0.5,0.5, 0.75), t.col="black"))
# close the file
snpgdsClose(genofile)
Example output
Loading required package: gdsfmt
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
Individual dissimilarity analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Dissimilarity: the sum of all selected genotypes (0,1,2) = 2446510
Dissimilarity: Wed Jan 6 22:17:21 2021 0%
Dissimilarity: Wed Jan 6 22:17:22 2021 100%
Determine groups by permutation (Z threshold: 15, outlier threshold: 5):
Create 3 groups.
$sample.id
[1] "NA19152" "NA19139" "NA18912" "NA19160" "NA07034"
[6] "NA07055" "NA12814" "NA10847" "NA18532" "NA18561"
[11] "NA18942" "NA18940" "NA18515" "NA19222" "NA18508"
[16] "NA19129" "NA12056" "NA10863" "NA10857" "NA12006"
[21] "NA18605" "NA18542" "NA18945" "NA18949" "NA19238"
[26] "NA19194" "NA19142" "NA18913" "NA12145" "NA12763"
[31] "NA07357" "NA12144" "NA18550" "NA18608" "NA18964"
[36] "NA18953" "NA19154" "NA19138" "NA18852" "NA19120"
[41] "NA07019" "NA10831" "NA07000" "NA11832" "NA18564"
[46] "NA18961" "NA18972" "NA19210" "NA19204" "NA18507"
[51] "NA19159" "NA06991" "NA11840" "NA12802" "NA12813"
[56] "NA18571" "NA18620" "NA18967" "NA18976" "NA19211"
[61] "NA18516" "NA18523" "NA12761" "NA10830" "NA10855"
[66] "NA18623" "NA18576" "NA18981" "NA18971" "NA18862"
[71] "NA19205" "NA19101" "NA19102" "NA06994" "NA11993"
[76] "NA11995" "NA12891" "NA18582" "NA18633" "NA18994"
[81] "NA18872" "NA19192" "NA19172" "NA19092" "NA12864"
[86] "NA12751" "NA10839" "NA12717" "NA18637" "NA18594"
[91] "NA18998" "NA19000" "NA12753" "NA12707" "NA11839"
[96] "NA10859" "NA18526" "NA18524" "NA18529" "NA18558"
[101] "NA18502" "NA19145" "NA18505" "NA18856" "NA12875"
[106] "NA12156.dup" "NA12156" "NA07056" "NA18562" "NA18537"
[111] "NA18603" "NA18540" "NA19153" "NA19137" "NA19202"
[116] "NA19239" "NA12044" "NA11992" "NA11829" "NA07022"
[121] "NA18545" "NA18572" "NA18547" "NA18609.dup" "NA18857"
[126] "NA19238.dup" "NA18501" "NA19240" "NA06993.dup" "NA12239"
[131] "NA12154" "NA12762" "NA18609" "NA18552" "NA18611"
[136] "NA18555" "NA19223" "NA18500" "NA18861" "NA12716"
[141] "NA12878" "NA10856" "NA12874" "NA18566" "NA18563"
[146] "NA18570" "NA18612" "NA19201" "NA19144" "NA19193"
[151] "NA18503" "NA12760" "NA11993.dup" "NA06985" "NA12003"
[156] "NA18621" "NA18594.dup" "NA18622" "NA18573" "NA18504"
[161] "NA19203" "NA19143" "NA18871" "NA07348" "NA12750"
[166] "NA11831" "NA10835" "NA18577" "NA18624" "NA18579"
[171] "NA18632" "NA18870" "NA19200" "NA18517" "NA19221"
[176] "NA12146" "NA11882" "NA18635" "NA18592" "NA18636"
[181] "NA18593" "NA18863" "NA18855" "NA18862.dup" "NA19209"
[186] "NA18951.dup" "NA18943" "NA18947" "NA18944" "NA18521"
[191] "NA18858" "NA19141" "NA19093" "NA10861" "NA12005"
[196] "NA10851" "NA12234" "NA18948" "NA18951" "NA18952"
[201] "NA18956" "NA19099" "NA18854" "NA19132" "NA12004"
[206] "NA07345" "NA07029" "NA12892" "NA18968" "NA18959"
[211] "NA18969" "NA18960" "NA19206" "NA18506" "NA19098"
[216] "NA19130" "NA07048" "NA10854" "NA12248" "NA10846"
[221] "NA18965" "NA18973" "NA18966" "NA18975" "NA19128"
[226] "NA19131" "NA18522" "NA19208" "NA12801" "NA12872"
[231] "NA12155" "NA06993" "NA18978" "NA18970" "NA18980"
[236] "NA18995.dup" "NA18859.dup" "NA19116" "NA18914" "NA19127"
[241] "NA11830" "NA12865" "NA10838" "NA12249" "NA18974"
[246] "NA18987" "NA18990" "NA18991" "NA19094" "NA19161"
[251] "NA18853" "NA19173" "NA12057" "NA10860" "NA12812"
[256] "NA11881" "NA18992" "NA18995" "NA18997" "NA19012"
[261] "NA19171" "NA19140" "NA18859" "NA19119" "NA11994"
[266] "NA12873" "NA12815" "NA19005" "NA18999" "NA19007"
[271] "NA19003" "NA18860" "NA19207" "NA19100" "NA19103"
[276] "NA12740" "NA12752" "NA12043" "NA12264"
$z.threshold
[1] 15
$outlier.n
[1] 5
$samp.order
[1] 83 252 261 1 37 113 50 15 214 227 62 190 251 39 203 139 182 70
[19] 184 226 204 216 82 26 150 237 263 191 272 114 2 38 193 84 249 72
[37] 73 275 162 102 149 48 60 185 240 16 225 51 4 250 104 125 183 262
[55] 27 192 273 213 228 215 202 274 3 116 128 25 126 28 239 137 14 175
[73] 101 127 138 173 115 148 172 81 163 238 40 264 161 49 71 103 151 160
[91] 61 13 174 198 171 180 78 9 33 124 133 110 144 56 269 24 257 91
[109] 233 212 260 11 247 146 147 99 109 67 111 169 34 21 178 89 168 156
[127] 10 22 98 100 145 179 136 79 121 57 181 112 246 201 268 245 122 259
[145] 158 187 47 92 46 270 35 234 224 90 157 68 222 200 97 134 248 235
[163] 186 199 170 223 36 189 221 188 210 58 12 209 80 236 258 23 271 69
[181] 211 123 45 59 135 66 159 265 76 194 152 63 277 205 155 243 53 95
[199] 218 30 93 132 5 6 217 75 153 118 254 129 232 52 154 108 41 120
[217] 208 77 141 7 54 267 86 165 276 20 87 195 117 19 278 105 143 242
[235] 140 88 94 197 18 279 106 107 42 231 74 43 207 241 119 142 253 17
[253] 196 130 8 176 64 131 166 44 65 32 29 220 55 229 255 177 96 256
[271] 230 85 266 219 167 244 31 164 206
$samp.group
[1] G001 G001 G001 G001 G003 G003 G003 G003 G002 G002 G002 G002 G001 G001 G001
[16] G001 G003 G003 G003 G003 G002 G002 G002 G002 G001 G001 G001 G001 G003 G003
[31] G003 G003 G002 G002 G002 G002 G001 G001 G001 G001 G003 G003 G003 G003 G002
[46] G002 G002 G001 G001 G001 G001 G003 G003 G003 G003 G002 G002 G002 G002 G001
[61] G001 G001 G003 G003 G003 G002 G002 G002 G002 G001 G001 G001 G001 G003 G003
[76] G003 G003 G002 G002 G002 G001 G001 G001 G001 G003 G003 G003 G003 G002 G002
[91] G002 G002 G003 G003 G003 G003 G002 G002 G002 G002 G001 G001 G001 G001 G003
[106] G003 G003 G003 G002 G002 G002 G002 G001 G001 G001 G001 G003 G003 G003 G003
[121] G002 G002 G002 G002 G001 G001 G001 G001 G003 G003 G003 G003 G002 G002 G002
[136] G002 G001 G001 G001 G003 G003 G003 G003 G002 G002 G002 G002 G001 G001 G001
[151] G001 G003 G003 G003 G003 G002 G002 G002 G002 G001 G001 G001 G001 G003 G003
[166] G003 G003 G002 G002 G002 G002 G001 G001 G001 G001 G003 G003 G002 G002 G002
[181] G002 G001 G001 G001 G001 G002 G002 G002 G002 G001 G001 G001 G001 G003 G003
[196] G003 G003 G002 G002 G002 G002 G001 G001 G001 G003 G003 G003 G003 G002 G002
[211] G002 G002 G001 G001 G001 G001 G003 G003 G003 G003 G002 G002 G002 G002 G001
[226] G001 G001 G001 G003 G003 G003 G003 G002 G002 G002 G002 G001 G001 G001 G001
[241] G003 G003 G003 G003 G002 G002 G002 G002 G001 G001 G001 G001 G003 G003 G003
[256] G003 G002 G002 G002 G002 G001 G001 G001 G001 G003 G003 G003 G002 G002 G002
[271] G002 G001 G001 G001 G001 G003 G003 G003 G003
Levels: G001 G002 G003
$dmat
G001 G002 G003
G001 0.9532539 1.0965483 1.0956439
G002 1.0965483 0.8313777 0.9752263
G003 1.0956439 0.9752263 0.8966300
$dendrogram
'dendrogram' with 2 branches and 279 members total, at height 1.096101
$merge
z n1 n2
1 0.0000000 1 1
2 0.0000000 1 1
3 0.0000000 1 1
4 0.0000000 1 1
5 0.0000000 1 1
6 0.0000000 1 1
7 0.0000000 1 1
8 0.0000000 1 1
9 0.0000000 1 1
10 0.0000000 1 1
11 0.0000000 1 1
12 0.0000000 1 1
13 0.0000000 1 1
14 0.0000000 1 1
15 0.0000000 1 1
16 0.0000000 1 1
17 0.0000000 1 1
18 0.0000000 1 1
19 0.0000000 1 1
20 0.0000000 1 1
21 0.0000000 1 1
22 0.0000000 1 1
23 0.0000000 1 1
24 0.0000000 1 1
25 0.0000000 1 1
26 0.0000000 1 1
27 0.0000000 1 1
28 0.0000000 1 1
29 0.0000000 1 1
30 0.0000000 1 1
31 0.0000000 1 1
32 0.0000000 1 1
33 0.0000000 1 1
34 0.0000000 1 1
35 0.0000000 1 1
36 0.0000000 1 1
37 0.0000000 1 1
38 0.0000000 1 1
39 0.0000000 1 1
40 0.0000000 1 1
41 0.0000000 1 1
42 0.0000000 1 1
43 0.0000000 1 1
44 0.0000000 1 1
45 0.0000000 1 1
46 0.0000000 1 1
47 0.0000000 1 1
48 0.0000000 1 1
49 0.0000000 1 1
50 0.0000000 1 1
51 0.0000000 1 1
52 0.0000000 1 1
53 0.0000000 1 1
54 0.0000000 1 1
55 0.0000000 1 1
56 0.0000000 1 1
57 0.0000000 1 1
58 0.0000000 1 1
59 0.0000000 1 1
60 0.0000000 1 1
61 1.4569172 1 2
62 0.0000000 1 1
63 0.0000000 1 1
64 0.0000000 1 1
65 0.0000000 1 1
66 0.0000000 1 1
67 0.0000000 1 1
68 0.0000000 1 1
69 0.0000000 1 1
70 0.0000000 1 1
71 1.4449585 2 2
72 0.7117858 1 2
73 0.7275347 1 2
74 0.7273380 1 2
75 0.7689553 1 2
76 0.7365853 1 2
77 0.7152495 1 2
78 0.7148537 1 2
79 0.7575992 1 2
80 0.7248823 1 2
81 0.7261343 1 2
82 0.7107089 1 2
83 0.7059547 1 2
84 0.7305831 1 2
85 0.7347306 1 2
86 0.7132183 1 2
87 1.4562490 2 2
88 0.7089801 1 2
89 1.4037253 2 2
90 0.7220267 1 2
91 0.7411477 1 2
92 0.7144521 1 2
93 0.7300025 1 2
94 0.7045788 1 2
95 0.7546066 1 2
96 0.0000000 1 1
97 0.7352917 1 2
98 1.4616206 2 2
99 0.0000000 1 1
100 0.7559686 1 2
101 1.3981013 1 2
102 0.7381826 1 2
103 0.7343906 1 2
104 0.0000000 1 1
105 1.1946910 1 2
106 0.0000000 1 1
107 0.0000000 1 1
108 0.0000000 1 1
109 0.0000000 1 1
110 0.0000000 1 1
111 0.0000000 1 1
112 1.0286414 1 3
113 0.0000000 1 1
114 0.0000000 1 1
115 0.0000000 1 1
116 1.4075217 1 2
117 1.5224299 1 3
118 0.0000000 1 1
119 0.0000000 1 1
120 1.4159969 1 2
121 1.1568291 2 2
122 1.2851068 1 4
123 1.4106846 1 2
124 0.0000000 1 1
125 0.7365791 1 2
126 0.0000000 1 1
127 0.0000000 1 1
128 1.7649724 2 3
129 1.4247622 4 5
130 0.9086049 1 2
131 1.4267748 1 2
132 1.3227807 1 2
133 0.0000000 1 1
134 0.0000000 1 1
135 1.2308343 2 2
136 1.3195131 3 4
137 0.9744259 1 3
138 1.2650334 3 5
139 0.0000000 1 1
140 0.0000000 1 1
141 0.9992920 1 2
142 1.0842204 9 2
143 0.0000000 1 1
144 0.0000000 1 1
145 0.0000000 1 1
146 2.1751247 8 11
147 0.0000000 1 1
148 2.2765449 4 3
149 0.7394863 1 2
150 1.6351464 1 3
151 1.2667413 2 2
152 0.0000000 1 1
153 1.3825202 3 7
154 0.0000000 1 1
155 3.0150189 19 10
156 2.7530660 3 4
157 0.0000000 1 1
158 0.9375641 1 2
159 2.0899315 4 29
160 1.3014662 1 2
161 2.0923566 4 33
162 1.4105440 1 7
163 2.2398236 2 7
164 0.7574411 1 2
165 0.7208835 1 2
166 1.3677347 1 2
167 2.2370415 2 9
168 2.0779231 2 37
169 4.8159240 8 11
170 0.7307508 1 2
171 1.4902405 1 39
172 2.0252288 2 40
173 5.7537895 19 42
174 0.7088630 1 2
175 2.2755079 2 3
176 2.0754548 3 3
177 1.5814525 2 5
178 3.1017651 61 6
179 0.0000000 1 1
180 0.7477703 1 2
181 3.3386462 7 67
182 1.8425567 2 74
183 0.7069893 1 2
184 1.8007846 2 76
185 0.0000000 1 1
186 0.0000000 1 1
187 0.7016553 1 2
188 1.4183228 1 2
189 2.2511535 2 78
190 2.2389373 2 80
191 0.7226110 1 2
192 2.2803096 2 82
193 0.7720612 1 2
194 2.2921206 2 84
195 0.7535293 1 2
196 2.9210921 3 86
197 1.6847157 1 89
198 1.7432102 1 90
199 0.7366455 1 2
200 0.7909925 1 2
201 2.9225612 2 91
202 0.7402145 1 2
203 0.7336314 1 2
204 0.7505889 1 2
205 2.3536143 1 93
206 0.7304067 1 2
207 0.7459735 1 2
208 0.8230214 1 2
209 0.6878292 1 2
210 0.7262134 1 2
211 0.7362767 1 2
212 1.3722708 2 2
213 0.7618462 1 2
214 0.7509534 1 2
215 0.7545973 1 2
216 0.7232046 1 2
217 2.2960758 2 4
218 1.7252188 1 3
219 2.3883671 3 3
220 2.2283869 3 3
221 2.8784643 3 6
222 2.8331170 4 3
223 2.0016060 2 3
224 2.3135630 3 3
225 3.2453311 3 9
226 3.0184727 4 6
227 3.4032258 3 12
228 2.3782695 3 3
229 2.2881827 3 3
230 3.6066056 3 15
231 3.2112973 3 10
232 4.2035537 5 18
233 4.4105249 6 23
234 2.8293170 3 6
235 6.1157980 13 29
236 4.3706686 6 42
237 2.8807091 3 4
238 5.0223996 9 48
239 3.0813581 3 57
240 2.3128117 3 3
241 2.9343107 3 60
242 4.8898994 7 63
243 4.3931075 7 70
244 2.9684581 3 77
245 3.0939511 3 80
246 5.5139037 6 83
247 1.5821956 1 6
248 4.7342949 3 89
249 2.1376020 3 3
250 3.5820692 3 7
251 2.3026921 3 3
252 2.2823732 3 3
253 4.3477018 10 6
254 2.3248296 3 3
255 2.2649940 3 3
256 2.3643592 3 3
257 3.1261532 3 16
258 2.7716230 3 6
259 3.1030904 3 19
260 2.8211907 3 6
261 4.3375448 6 22
262 2.7931292 3 6
263 3.3149933 4 6
264 5.2136192 28 9
265 3.3228278 4 9
266 4.9736823 9 37
267 5.9978223 13 46
268 5.7140441 10 59
269 2.3251032 3 3
270 2.8953113 3 69
271 2.7992312 3 6
272 5.3914263 72 9
273 3.0700506 3 81
274 3.0014295 3 84
275 2.9772642 3 87
276 3.7140769 3 90
277 122.2690280 94 92
278 61.0609703 93 186
$clust.count
cluster
G001 G002 G003
93 94 92
SNPRelate documentation built on Nov. 8, 2020, 5:31 p.m.
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Description Usage Arguments Details Value Author(s) See Also Examples
Description
Perform hierarchical cluster analysis on the dissimilarity matrix.
Usage
1 | snpgdsHCluster(dist, sample.id=NULL, need.mat=TRUE, hang=0.25)
|
Arguments
dist |
an object of "snpgdsDissClass" from |
sample.id |
to specify sample id, only work if dist is a matrix |
need.mat |
if TRUE, store the dissimilarity matrix in the result |
hang |
The fraction of the plot height by which labels should hang below the rest of the plot. A negative value will cause the labels to hang down from 0. |
Details
Call the function hclust to perform hierarchical cluster
analysis, using method="average".
Value
Return a list (class "snpgdsHCClass"):
sample.id |
the sample ids used in the analysis |
hclust |
an object returned from |
dendrogram |
|
dist |
the dissimilarity matrix, if |
Author(s)
Xiuwen Zheng
See Also
snpgdsIBS, snpgdsDiss,
snpgdsCutTree
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 | # open an example dataset (HapMap)
genofile <- snpgdsOpen(snpgdsExampleFileName())
pop.group <- read.gdsn(index.gdsn(genofile, "sample.annot/pop.group"))
pop.group <- as.factor(pop.group)
pop.level <- levels(pop.group)
diss <- snpgdsDiss(genofile)
hc <- snpgdsHCluster(diss)
rv <- snpgdsCutTree(hc)
rv
# call 'plot' to draw a dendrogram
plot(rv$dendrogram, leaflab="none", main="HapMap Phase II")
# the distribution of Z scores
snpgdsDrawTree(rv, type="z-score", main="HapMap Phase II")
# draw dendrogram
snpgdsDrawTree(rv, main="HapMap Phase II",
edgePar=list(col=rgb(0.5,0.5,0.5, 0.75), t.col="black"))
# close the file
snpgdsClose(genofile)
|
Example output
Loading required package: gdsfmt
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
Individual dissimilarity analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Dissimilarity: the sum of all selected genotypes (0,1,2) = 2446510
Dissimilarity: Wed Jan 6 22:17:21 2021 0%
Dissimilarity: Wed Jan 6 22:17:22 2021 100%
Determine groups by permutation (Z threshold: 15, outlier threshold: 5):
Create 3 groups.
$sample.id
[1] "NA19152" "NA19139" "NA18912" "NA19160" "NA07034"
[6] "NA07055" "NA12814" "NA10847" "NA18532" "NA18561"
[11] "NA18942" "NA18940" "NA18515" "NA19222" "NA18508"
[16] "NA19129" "NA12056" "NA10863" "NA10857" "NA12006"
[21] "NA18605" "NA18542" "NA18945" "NA18949" "NA19238"
[26] "NA19194" "NA19142" "NA18913" "NA12145" "NA12763"
[31] "NA07357" "NA12144" "NA18550" "NA18608" "NA18964"
[36] "NA18953" "NA19154" "NA19138" "NA18852" "NA19120"
[41] "NA07019" "NA10831" "NA07000" "NA11832" "NA18564"
[46] "NA18961" "NA18972" "NA19210" "NA19204" "NA18507"
[51] "NA19159" "NA06991" "NA11840" "NA12802" "NA12813"
[56] "NA18571" "NA18620" "NA18967" "NA18976" "NA19211"
[61] "NA18516" "NA18523" "NA12761" "NA10830" "NA10855"
[66] "NA18623" "NA18576" "NA18981" "NA18971" "NA18862"
[71] "NA19205" "NA19101" "NA19102" "NA06994" "NA11993"
[76] "NA11995" "NA12891" "NA18582" "NA18633" "NA18994"
[81] "NA18872" "NA19192" "NA19172" "NA19092" "NA12864"
[86] "NA12751" "NA10839" "NA12717" "NA18637" "NA18594"
[91] "NA18998" "NA19000" "NA12753" "NA12707" "NA11839"
[96] "NA10859" "NA18526" "NA18524" "NA18529" "NA18558"
[101] "NA18502" "NA19145" "NA18505" "NA18856" "NA12875"
[106] "NA12156.dup" "NA12156" "NA07056" "NA18562" "NA18537"
[111] "NA18603" "NA18540" "NA19153" "NA19137" "NA19202"
[116] "NA19239" "NA12044" "NA11992" "NA11829" "NA07022"
[121] "NA18545" "NA18572" "NA18547" "NA18609.dup" "NA18857"
[126] "NA19238.dup" "NA18501" "NA19240" "NA06993.dup" "NA12239"
[131] "NA12154" "NA12762" "NA18609" "NA18552" "NA18611"
[136] "NA18555" "NA19223" "NA18500" "NA18861" "NA12716"
[141] "NA12878" "NA10856" "NA12874" "NA18566" "NA18563"
[146] "NA18570" "NA18612" "NA19201" "NA19144" "NA19193"
[151] "NA18503" "NA12760" "NA11993.dup" "NA06985" "NA12003"
[156] "NA18621" "NA18594.dup" "NA18622" "NA18573" "NA18504"
[161] "NA19203" "NA19143" "NA18871" "NA07348" "NA12750"
[166] "NA11831" "NA10835" "NA18577" "NA18624" "NA18579"
[171] "NA18632" "NA18870" "NA19200" "NA18517" "NA19221"
[176] "NA12146" "NA11882" "NA18635" "NA18592" "NA18636"
[181] "NA18593" "NA18863" "NA18855" "NA18862.dup" "NA19209"
[186] "NA18951.dup" "NA18943" "NA18947" "NA18944" "NA18521"
[191] "NA18858" "NA19141" "NA19093" "NA10861" "NA12005"
[196] "NA10851" "NA12234" "NA18948" "NA18951" "NA18952"
[201] "NA18956" "NA19099" "NA18854" "NA19132" "NA12004"
[206] "NA07345" "NA07029" "NA12892" "NA18968" "NA18959"
[211] "NA18969" "NA18960" "NA19206" "NA18506" "NA19098"
[216] "NA19130" "NA07048" "NA10854" "NA12248" "NA10846"
[221] "NA18965" "NA18973" "NA18966" "NA18975" "NA19128"
[226] "NA19131" "NA18522" "NA19208" "NA12801" "NA12872"
[231] "NA12155" "NA06993" "NA18978" "NA18970" "NA18980"
[236] "NA18995.dup" "NA18859.dup" "NA19116" "NA18914" "NA19127"
[241] "NA11830" "NA12865" "NA10838" "NA12249" "NA18974"
[246] "NA18987" "NA18990" "NA18991" "NA19094" "NA19161"
[251] "NA18853" "NA19173" "NA12057" "NA10860" "NA12812"
[256] "NA11881" "NA18992" "NA18995" "NA18997" "NA19012"
[261] "NA19171" "NA19140" "NA18859" "NA19119" "NA11994"
[266] "NA12873" "NA12815" "NA19005" "NA18999" "NA19007"
[271] "NA19003" "NA18860" "NA19207" "NA19100" "NA19103"
[276] "NA12740" "NA12752" "NA12043" "NA12264"
$z.threshold
[1] 15
$outlier.n
[1] 5
$samp.order
[1] 83 252 261 1 37 113 50 15 214 227 62 190 251 39 203 139 182 70
[19] 184 226 204 216 82 26 150 237 263 191 272 114 2 38 193 84 249 72
[37] 73 275 162 102 149 48 60 185 240 16 225 51 4 250 104 125 183 262
[55] 27 192 273 213 228 215 202 274 3 116 128 25 126 28 239 137 14 175
[73] 101 127 138 173 115 148 172 81 163 238 40 264 161 49 71 103 151 160
[91] 61 13 174 198 171 180 78 9 33 124 133 110 144 56 269 24 257 91
[109] 233 212 260 11 247 146 147 99 109 67 111 169 34 21 178 89 168 156
[127] 10 22 98 100 145 179 136 79 121 57 181 112 246 201 268 245 122 259
[145] 158 187 47 92 46 270 35 234 224 90 157 68 222 200 97 134 248 235
[163] 186 199 170 223 36 189 221 188 210 58 12 209 80 236 258 23 271 69
[181] 211 123 45 59 135 66 159 265 76 194 152 63 277 205 155 243 53 95
[199] 218 30 93 132 5 6 217 75 153 118 254 129 232 52 154 108 41 120
[217] 208 77 141 7 54 267 86 165 276 20 87 195 117 19 278 105 143 242
[235] 140 88 94 197 18 279 106 107 42 231 74 43 207 241 119 142 253 17
[253] 196 130 8 176 64 131 166 44 65 32 29 220 55 229 255 177 96 256
[271] 230 85 266 219 167 244 31 164 206
$samp.group
[1] G001 G001 G001 G001 G003 G003 G003 G003 G002 G002 G002 G002 G001 G001 G001
[16] G001 G003 G003 G003 G003 G002 G002 G002 G002 G001 G001 G001 G001 G003 G003
[31] G003 G003 G002 G002 G002 G002 G001 G001 G001 G001 G003 G003 G003 G003 G002
[46] G002 G002 G001 G001 G001 G001 G003 G003 G003 G003 G002 G002 G002 G002 G001
[61] G001 G001 G003 G003 G003 G002 G002 G002 G002 G001 G001 G001 G001 G003 G003
[76] G003 G003 G002 G002 G002 G001 G001 G001 G001 G003 G003 G003 G003 G002 G002
[91] G002 G002 G003 G003 G003 G003 G002 G002 G002 G002 G001 G001 G001 G001 G003
[106] G003 G003 G003 G002 G002 G002 G002 G001 G001 G001 G001 G003 G003 G003 G003
[121] G002 G002 G002 G002 G001 G001 G001 G001 G003 G003 G003 G003 G002 G002 G002
[136] G002 G001 G001 G001 G003 G003 G003 G003 G002 G002 G002 G002 G001 G001 G001
[151] G001 G003 G003 G003 G003 G002 G002 G002 G002 G001 G001 G001 G001 G003 G003
[166] G003 G003 G002 G002 G002 G002 G001 G001 G001 G001 G003 G003 G002 G002 G002
[181] G002 G001 G001 G001 G001 G002 G002 G002 G002 G001 G001 G001 G001 G003 G003
[196] G003 G003 G002 G002 G002 G002 G001 G001 G001 G003 G003 G003 G003 G002 G002
[211] G002 G002 G001 G001 G001 G001 G003 G003 G003 G003 G002 G002 G002 G002 G001
[226] G001 G001 G001 G003 G003 G003 G003 G002 G002 G002 G002 G001 G001 G001 G001
[241] G003 G003 G003 G003 G002 G002 G002 G002 G001 G001 G001 G001 G003 G003 G003
[256] G003 G002 G002 G002 G002 G001 G001 G001 G001 G003 G003 G003 G002 G002 G002
[271] G002 G001 G001 G001 G001 G003 G003 G003 G003
Levels: G001 G002 G003
$dmat
G001 G002 G003
G001 0.9532539 1.0965483 1.0956439
G002 1.0965483 0.8313777 0.9752263
G003 1.0956439 0.9752263 0.8966300
$dendrogram
'dendrogram' with 2 branches and 279 members total, at height 1.096101
$merge
z n1 n2
1 0.0000000 1 1
2 0.0000000 1 1
3 0.0000000 1 1
4 0.0000000 1 1
5 0.0000000 1 1
6 0.0000000 1 1
7 0.0000000 1 1
8 0.0000000 1 1
9 0.0000000 1 1
10 0.0000000 1 1
11 0.0000000 1 1
12 0.0000000 1 1
13 0.0000000 1 1
14 0.0000000 1 1
15 0.0000000 1 1
16 0.0000000 1 1
17 0.0000000 1 1
18 0.0000000 1 1
19 0.0000000 1 1
20 0.0000000 1 1
21 0.0000000 1 1
22 0.0000000 1 1
23 0.0000000 1 1
24 0.0000000 1 1
25 0.0000000 1 1
26 0.0000000 1 1
27 0.0000000 1 1
28 0.0000000 1 1
29 0.0000000 1 1
30 0.0000000 1 1
31 0.0000000 1 1
32 0.0000000 1 1
33 0.0000000 1 1
34 0.0000000 1 1
35 0.0000000 1 1
36 0.0000000 1 1
37 0.0000000 1 1
38 0.0000000 1 1
39 0.0000000 1 1
40 0.0000000 1 1
41 0.0000000 1 1
42 0.0000000 1 1
43 0.0000000 1 1
44 0.0000000 1 1
45 0.0000000 1 1
46 0.0000000 1 1
47 0.0000000 1 1
48 0.0000000 1 1
49 0.0000000 1 1
50 0.0000000 1 1
51 0.0000000 1 1
52 0.0000000 1 1
53 0.0000000 1 1
54 0.0000000 1 1
55 0.0000000 1 1
56 0.0000000 1 1
57 0.0000000 1 1
58 0.0000000 1 1
59 0.0000000 1 1
60 0.0000000 1 1
61 1.4569172 1 2
62 0.0000000 1 1
63 0.0000000 1 1
64 0.0000000 1 1
65 0.0000000 1 1
66 0.0000000 1 1
67 0.0000000 1 1
68 0.0000000 1 1
69 0.0000000 1 1
70 0.0000000 1 1
71 1.4449585 2 2
72 0.7117858 1 2
73 0.7275347 1 2
74 0.7273380 1 2
75 0.7689553 1 2
76 0.7365853 1 2
77 0.7152495 1 2
78 0.7148537 1 2
79 0.7575992 1 2
80 0.7248823 1 2
81 0.7261343 1 2
82 0.7107089 1 2
83 0.7059547 1 2
84 0.7305831 1 2
85 0.7347306 1 2
86 0.7132183 1 2
87 1.4562490 2 2
88 0.7089801 1 2
89 1.4037253 2 2
90 0.7220267 1 2
91 0.7411477 1 2
92 0.7144521 1 2
93 0.7300025 1 2
94 0.7045788 1 2
95 0.7546066 1 2
96 0.0000000 1 1
97 0.7352917 1 2
98 1.4616206 2 2
99 0.0000000 1 1
100 0.7559686 1 2
101 1.3981013 1 2
102 0.7381826 1 2
103 0.7343906 1 2
104 0.0000000 1 1
105 1.1946910 1 2
106 0.0000000 1 1
107 0.0000000 1 1
108 0.0000000 1 1
109 0.0000000 1 1
110 0.0000000 1 1
111 0.0000000 1 1
112 1.0286414 1 3
113 0.0000000 1 1
114 0.0000000 1 1
115 0.0000000 1 1
116 1.4075217 1 2
117 1.5224299 1 3
118 0.0000000 1 1
119 0.0000000 1 1
120 1.4159969 1 2
121 1.1568291 2 2
122 1.2851068 1 4
123 1.4106846 1 2
124 0.0000000 1 1
125 0.7365791 1 2
126 0.0000000 1 1
127 0.0000000 1 1
128 1.7649724 2 3
129 1.4247622 4 5
130 0.9086049 1 2
131 1.4267748 1 2
132 1.3227807 1 2
133 0.0000000 1 1
134 0.0000000 1 1
135 1.2308343 2 2
136 1.3195131 3 4
137 0.9744259 1 3
138 1.2650334 3 5
139 0.0000000 1 1
140 0.0000000 1 1
141 0.9992920 1 2
142 1.0842204 9 2
143 0.0000000 1 1
144 0.0000000 1 1
145 0.0000000 1 1
146 2.1751247 8 11
147 0.0000000 1 1
148 2.2765449 4 3
149 0.7394863 1 2
150 1.6351464 1 3
151 1.2667413 2 2
152 0.0000000 1 1
153 1.3825202 3 7
154 0.0000000 1 1
155 3.0150189 19 10
156 2.7530660 3 4
157 0.0000000 1 1
158 0.9375641 1 2
159 2.0899315 4 29
160 1.3014662 1 2
161 2.0923566 4 33
162 1.4105440 1 7
163 2.2398236 2 7
164 0.7574411 1 2
165 0.7208835 1 2
166 1.3677347 1 2
167 2.2370415 2 9
168 2.0779231 2 37
169 4.8159240 8 11
170 0.7307508 1 2
171 1.4902405 1 39
172 2.0252288 2 40
173 5.7537895 19 42
174 0.7088630 1 2
175 2.2755079 2 3
176 2.0754548 3 3
177 1.5814525 2 5
178 3.1017651 61 6
179 0.0000000 1 1
180 0.7477703 1 2
181 3.3386462 7 67
182 1.8425567 2 74
183 0.7069893 1 2
184 1.8007846 2 76
185 0.0000000 1 1
186 0.0000000 1 1
187 0.7016553 1 2
188 1.4183228 1 2
189 2.2511535 2 78
190 2.2389373 2 80
191 0.7226110 1 2
192 2.2803096 2 82
193 0.7720612 1 2
194 2.2921206 2 84
195 0.7535293 1 2
196 2.9210921 3 86
197 1.6847157 1 89
198 1.7432102 1 90
199 0.7366455 1 2
200 0.7909925 1 2
201 2.9225612 2 91
202 0.7402145 1 2
203 0.7336314 1 2
204 0.7505889 1 2
205 2.3536143 1 93
206 0.7304067 1 2
207 0.7459735 1 2
208 0.8230214 1 2
209 0.6878292 1 2
210 0.7262134 1 2
211 0.7362767 1 2
212 1.3722708 2 2
213 0.7618462 1 2
214 0.7509534 1 2
215 0.7545973 1 2
216 0.7232046 1 2
217 2.2960758 2 4
218 1.7252188 1 3
219 2.3883671 3 3
220 2.2283869 3 3
221 2.8784643 3 6
222 2.8331170 4 3
223 2.0016060 2 3
224 2.3135630 3 3
225 3.2453311 3 9
226 3.0184727 4 6
227 3.4032258 3 12
228 2.3782695 3 3
229 2.2881827 3 3
230 3.6066056 3 15
231 3.2112973 3 10
232 4.2035537 5 18
233 4.4105249 6 23
234 2.8293170 3 6
235 6.1157980 13 29
236 4.3706686 6 42
237 2.8807091 3 4
238 5.0223996 9 48
239 3.0813581 3 57
240 2.3128117 3 3
241 2.9343107 3 60
242 4.8898994 7 63
243 4.3931075 7 70
244 2.9684581 3 77
245 3.0939511 3 80
246 5.5139037 6 83
247 1.5821956 1 6
248 4.7342949 3 89
249 2.1376020 3 3
250 3.5820692 3 7
251 2.3026921 3 3
252 2.2823732 3 3
253 4.3477018 10 6
254 2.3248296 3 3
255 2.2649940 3 3
256 2.3643592 3 3
257 3.1261532 3 16
258 2.7716230 3 6
259 3.1030904 3 19
260 2.8211907 3 6
261 4.3375448 6 22
262 2.7931292 3 6
263 3.3149933 4 6
264 5.2136192 28 9
265 3.3228278 4 9
266 4.9736823 9 37
267 5.9978223 13 46
268 5.7140441 10 59
269 2.3251032 3 3
270 2.8953113 3 69
271 2.7992312 3 6
272 5.3914263 72 9
273 3.0700506 3 81
274 3.0014295 3 84
275 2.9772642 3 87
276 3.7140769 3 90
277 122.2690280 94 92
278 61.0609703 93 186
$clust.count
cluster
G001 G002 G003
93 94 92
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