exprmclust: exprmclust
In TSCAN: Tools for Single-Cell Analysis
Description
Usage
Arguments
Details
Value
Author(s)
References
Examples
Description
Perform model-based clustering on expression values
Usage
1
exprmclust(data, clusternum = 2:9, modelNames = "VVV", reduce = T)
Arguments
data
The raw single_cell data, which is a numeric matrix or data.frame. Rows represent genes/features and columns represent single cells.
clusternum
An integer vector specifying all possible cluster numbers. The best cluster number will be picked using BIC. The minimum value should be two other
modelNames
model to be used in model-based clustering. By default "ellipsoidal, varying volume, shape, and orientation" is used.
reduce
Whether to perform the PCA on the expression data.
Details
By default, this function first uses principal component analysis (PCA) to reduce dimensionality of original data.
It then performs model-based clustering on the transformed expression values.
A minimum-spanning-tree is constructed to link the cluster centers.
The clustering results will be used for TSCAN ordering.
Value
if more than one cluster detected, a list containing
pcareduceres Numeric matrix containing the transformed expression values after PCA.
MSTtree igraph object which is the result of constructing MST.
clusterid A named vector specifying which cluster the cells belong to.
clucenter Numeric matrix of the cluster centers.
if only one cluster detected, a list containing
pcareduceres Numeric matrix containing the transformed expression values after PCA.
Author(s)
Zhicheng Ji, Hongkai Ji <zji4@zji4.edu>
References
Fraley, C., & Raftery, A. E. (2002). Model-based clustering, discriminant analysis, and density estimation. Journal of the American Statistical Association, 97(458), 611-631.
Examples
1
2
3
data(lpsdata)
procdata <- preprocess(lpsdata)
exprmclust(procdata)
Example output
$pcareduceres
PC1 PC2 PC3 PC4 PC5
Unstimulated_S15 -4.92638297 -8.8529185 3.22733252 -2.530967511 -2.32018858
Unstimulated_S16 -6.53424105 2.7790245 -0.07747889 0.828806525 1.38991796
Unstimulated_S17 -4.37822709 -7.1209402 3.75669380 -1.880575370 -0.20894592
Unstimulated_S18 17.81566572 -4.9989393 5.89433717 0.498551168 0.37654921
Unstimulated_S23 4.63958402 -7.0623736 -0.16541202 1.884503386 -4.20403502
Unstimulated_S24 -5.11519374 -7.8997135 3.39796650 -3.705876957 -0.72953511
Unstimulated_S26 -5.61797356 -7.0595907 0.59760040 -0.830618710 -4.50418081
Unstimulated_S27 -16.00062653 -3.1312633 -0.71870458 1.113940481 -2.63587791
Unstimulated_S28 -7.66518422 -8.1902394 1.26091879 -2.130027451 -5.02037825
Unstimulated_S2 -7.01346590 -5.4934888 -1.37784833 1.466572277 4.56611985
Unstimulated_S31 -2.96507054 -3.5346277 -0.64206453 5.027971580 4.34014341
Unstimulated_S32 -2.61022408 -4.4616316 -1.10533938 0.434571738 4.00092481
Unstimulated_S34 -7.21965614 -4.0424538 -4.26155077 2.719748564 1.25508809
Unstimulated_S37 16.95835092 -5.4442503 5.10034345 1.603287505 -0.74659474
Unstimulated_S38 -11.22916670 -6.1224529 -1.21729258 -0.267079854 -1.73711700
Unstimulated_S39 -8.59346505 -6.6919448 0.07142350 0.549971696 1.19148416
Unstimulated_S3 -9.23322744 -3.5455576 -2.70894287 3.510278152 0.33302224
Unstimulated_S41 -2.38737204 -4.3388880 0.33955341 -2.645652053 10.18993650
Unstimulated_S46 -9.94907597 -4.8907295 -2.99509140 2.355224934 -1.41274142
Unstimulated_S47 -0.31980414 -5.5103084 -2.42844969 -0.440886113 1.38752524
Unstimulated_S48 -4.85597695 -6.6271405 -0.78445250 0.464599295 -6.21643850
Unstimulated_S49 -8.52832342 -7.0757567 -0.23212922 -1.232910859 -0.04610125
Unstimulated_S4 -1.67313748 -4.0589471 -1.76452598 0.711142629 -0.32216581
Unstimulated_S51 -6.05022337 -5.2222314 -9.85843013 0.032263153 1.44143540
Unstimulated_S52 -6.46344442 -5.8367555 0.48176676 3.486264194 0.60760780
Unstimulated_S53 -5.63582158 -3.3383028 -0.05760304 1.476669275 2.06340185
Unstimulated_S54 -0.84628345 -6.1867255 -5.47061553 0.209137854 -2.77552085
Unstimulated_S55 11.32263613 -7.0996464 3.91329851 0.307710659 0.50135403
Unstimulated_S5 0.35007434 -2.5303971 -0.69994892 -1.999123649 4.25006301
Unstimulated_S60 -8.38574750 -8.0671125 1.35441912 -1.448207726 -0.12567796
Unstimulated_S61 -8.97361103 -5.9023228 0.67988538 4.960491262 -1.11922858
Unstimulated_S62 -0.54632004 -7.5029215 2.73790070 -2.444717075 -2.65743490
Unstimulated_S63 -9.00060740 -4.8634030 -0.71524850 2.479860400 0.85320474
Unstimulated_S66 -6.96045778 -7.5509841 -0.45159996 0.734743680 -3.27054592
Unstimulated_S6 -3.71662075 -8.8188517 3.01350227 -1.390360390 -1.58972241
Unstimulated_S70 -6.31449548 -4.7744833 -2.53975012 0.903786856 0.39503315
Unstimulated_S71 -5.20887527 -6.7001860 -0.54456262 1.400067578 2.55685691
Unstimulated_S72 0.06053991 -3.8589266 -1.38365411 6.023712402 3.16191871
Unstimulated_S74 -1.21926738 -7.3115827 1.94698254 -1.931832975 -0.81712112
Unstimulated_S75 -2.42607251 -7.3594098 -0.78034205 -0.386519407 2.42879469
Unstimulated_S76 -1.14472728 -5.7108653 -3.92242548 1.964556081 4.86660657
Unstimulated_S77 -1.91827615 -4.9925797 2.10799225 1.867632369 5.41470502
Unstimulated_S78 -9.11918319 -6.6336481 0.50797940 -3.363948549 0.57338160
Unstimulated_S79 4.71193963 -7.0725255 0.84396847 -3.113547137 2.84111610
Unstimulated_S7 15.02717140 -3.1812831 -20.37863291 -0.195088580 -3.81874672
Unstimulated_S80 -6.16676261 -4.3178415 -4.46734816 4.330139633 3.38227484
Unstimulated_S81 14.68838230 -4.8070524 5.95065699 3.154664077 2.03882286
Unstimulated_S82 -11.18519764 -5.1538116 1.38012271 -0.546715656 -2.40312946
Unstimulated_S83 7.86295942 -8.4072488 1.72028689 -2.583946521 0.95359758
Unstimulated_S84 12.45244947 -7.3521724 6.14909952 -0.644095292 3.28545509
Unstimulated_S85 17.77990759 -5.6904395 6.05606450 0.429767132 -0.08124407
Unstimulated_S8 0.48902448 -3.1708219 -8.27172906 -2.165200456 5.66737518
Unstimulated_S90 -7.04643419 -0.6512254 -0.51337113 0.004834302 3.04673465
Unstimulated_S92 -1.76995672 -5.1857664 0.50378468 6.754768765 1.37016863
Unstimulated_S93 -6.32462213 -6.8513650 -2.26678468 4.944123477 -3.39052517
Unstimulated_S95 15.90686277 -5.9030986 4.81258389 1.951157858 -1.48268050
Unstimulated_S96 -0.52027265 -5.8988891 2.93362818 -0.119240743 -4.71252497
LPS_6h_S10 3.41059912 4.8026164 0.85047833 1.780947630 2.24298684
LPS_6h_S11 -7.00637482 3.0573865 3.72876703 -4.809485380 -1.01143877
LPS_6h_S12 -4.95769809 3.8583591 0.58008114 -4.185700849 1.35934163
LPS_6h_S14 -0.07711724 4.3329526 3.15257157 -3.697925011 -1.57703436
LPS_6h_S15 -5.99004365 8.5170997 -1.98223087 -1.112486090 1.72521617
LPS_6h_S16 3.25273365 6.9835752 -2.50910046 -3.692120681 6.61555100
LPS_6h_S17 0.16567101 6.5309662 -1.76889325 8.012914146 3.22717809
LPS_6h_S18 3.91965487 4.4234775 0.25898982 -1.530347415 2.43127779
LPS_6h_S19 12.97789991 -0.5000554 -25.02491519 -1.781497016 -2.97902446
LPS_6h_S1 -7.03719726 7.3093473 -0.77765713 5.999730375 -0.53922083
LPS_6h_S20 -2.46467845 6.5408224 0.65057878 -3.523567289 -1.27990616
LPS_6h_S21 1.70142697 3.9383284 3.90496265 -2.314455582 0.58854748
LPS_6h_S22 -1.07460769 5.2207599 1.27816169 1.794528181 1.68747620
LPS_6h_S23 3.10603550 2.8995015 0.87847805 7.187948276 -2.40253086
LPS_6h_S24 2.75229554 6.4929678 4.28272143 1.379262311 2.22417765
LPS_6h_S25 -5.69985751 5.4299413 1.84199357 -5.745291220 0.76557472
LPS_6h_S26 2.71074604 7.2928612 -3.27872848 0.033622977 -1.24818749
LPS_6h_S27 2.90714330 6.2549945 1.06585578 4.290505200 2.31777167
LPS_6h_S28 -7.89316669 9.1771654 -1.93875068 6.521291494 -0.78088003
LPS_6h_S29 -4.46761743 6.4024421 -1.46099382 -4.947388517 1.68933704
LPS_6h_S2 -3.70134238 4.2744424 2.18699427 -3.738905322 -2.27810844
LPS_6h_S30 -7.67553517 8.8862112 -0.65398568 -1.856313382 -0.16399463
LPS_6h_S34 -3.55916101 6.2490548 -0.35526252 5.723292570 -2.82033325
LPS_6h_S35 10.26778553 0.4457759 -14.57019357 -3.176624180 -1.57986357
LPS_6h_S37 6.02404404 2.3526877 0.41900957 6.941185763 3.36490615
LPS_6h_S38 -2.48745627 3.0196229 1.72433835 -5.331153776 -0.78868036
LPS_6h_S39 -3.33697250 5.0115097 -0.47750058 -5.776854123 -3.53991962
LPS_6h_S3 -0.83089207 5.5145241 -1.01037500 -5.480371858 3.06046678
LPS_6h_S40 -1.81799956 8.1188865 0.03516849 3.021234920 -3.55901507
LPS_6h_S42 -1.65975486 6.9848698 0.04203313 -2.974717382 -0.76239455
LPS_6h_S43 1.33163332 0.5941597 4.86591317 -4.589921089 -3.17288891
LPS_6h_S44 3.85282419 3.4886721 1.01623599 -3.487203830 3.33621142
LPS_6h_S46 9.05482707 -1.0029173 5.80845865 -0.571412817 -0.78218627
LPS_6h_S48 -6.31474913 8.4861760 -0.86959683 0.815151097 -1.84176737
LPS_6h_S49 2.16789966 7.4756361 1.63731632 4.872575491 0.91741317
LPS_6h_S4 4.12396129 4.3565106 5.66052678 3.763670326 -4.61965416
LPS_6h_S50 5.05947785 3.1909071 -1.11006714 0.842027130 1.73581780
LPS_6h_S51 -3.60413100 5.9866181 0.66599037 1.456320190 -1.55938739
LPS_6h_S53 -1.87468034 3.9185788 0.87665262 -3.886568930 3.06134877
LPS_6h_S55 3.05305193 3.6942515 4.64567130 -1.659525273 0.17408672
LPS_6h_S56 16.02356893 -2.4976457 6.04171666 -0.778524362 -2.12019207
LPS_6h_S57 1.40436177 3.6939251 1.82268348 2.165641163 -3.37870649
LPS_6h_S58 -1.06997022 4.6632060 -3.01245754 -6.021806669 2.54405641
LPS_6h_S59 4.83412988 0.8066678 3.08974965 -1.002525091 -0.25579360
LPS_6h_S5 6.72565183 3.6389907 5.81248089 2.443312906 -2.09759812
LPS_6h_S60 8.58558030 0.3053119 5.96519081 0.754855349 0.98161175
LPS_6h_S61 8.62886105 0.9265787 5.58806183 1.165773221 -2.88207983
LPS_6h_S63 -3.71412623 6.4200202 0.15583612 1.784154397 1.78659200
LPS_6h_S64 3.70134435 5.2299460 1.10664240 3.591449839 -3.97923918
LPS_6h_S65 5.39827669 3.2897982 -2.30315801 -3.283495666 0.48639437
LPS_6h_S66 2.72151929 1.0535344 1.93643449 -8.168103819 3.23690978
LPS_6h_S67 13.72681695 0.1066333 -14.98690823 -0.121052195 -3.67368564
LPS_6h_S68 -4.29003096 6.2523365 3.01941856 -1.582325433 2.52132017
LPS_6h_S6 4.65411117 4.1693852 -1.97612448 -0.511589227 -3.11966973
LPS_6h_S70 1.65116754 3.5729276 6.06804155 -0.470158640 0.96624273
LPS_6h_S74 -0.03292703 1.9839559 3.27426863 -5.816737301 -1.17881452
LPS_6h_S76 -2.99857718 6.1842686 1.21836077 -4.259185554 1.04919203
LPS_6h_S77 4.71109312 6.8728790 -1.72215350 3.925529129 -4.45211994
LPS_6h_S78 12.97375958 -0.1385897 -14.76922619 -4.623364748 -2.15527185
LPS_6h_S79 14.81506369 -2.1037154 0.94989966 -2.204786844 -0.75277072
LPS_6h_S7 4.12414975 0.7361231 4.93784192 4.797098269 -2.78452929
LPS_6h_S80 -11.32182828 5.7084215 -2.80129888 4.149089105 -0.03603544
LPS_6h_S81 -1.27659653 1.1660312 1.41473961 -6.802943862 -5.72519432
LPS_6h_S83 16.36402421 -1.6575890 6.21153834 1.427235737 -0.73814919
LPS_6h_S84 -1.83424737 6.3887328 1.35240135 2.220242728 -4.49141816
LPS_6h_S86 6.56470875 4.0209304 -5.36589766 1.891070782 2.41680209
LPS_6h_S87 6.93158472 4.5905606 -4.89029618 5.173998039 5.14783421
LPS_6h_S88 -9.68164837 6.6423318 -1.42270777 -1.702127235 -3.04629747
LPS_6h_S89 2.65038377 8.6424984 -0.13397975 3.829378276 1.11653735
LPS_6h_S8 -3.68096328 4.3332544 1.53220666 -6.333910685 2.89330302
LPS_6h_S90 -8.58848657 9.5353756 0.65084652 -1.374325026 -1.21007512
LPS_6h_S91 9.01267053 0.5864734 1.08695356 -6.216677798 1.57159708
LPS_6h_S93 -6.55617226 4.9763087 4.31312777 -1.008142282 -5.76542630
LPS_6h_S9 4.22759613 7.1684539 3.62730613 5.808200530 1.50418649
$MSTtree
IGRAPH 37b136c UNW- 3 2 --
+ attr: name (v/c), weight (e/n)
+ edges from 37b136c (vertex names):
[1] 1--2 2--3
$clusterid
Unstimulated_S15 Unstimulated_S16 Unstimulated_S17 Unstimulated_S18
1 3 1 3
Unstimulated_S23 Unstimulated_S24 Unstimulated_S26 Unstimulated_S27
1 1 1 1
Unstimulated_S28 Unstimulated_S2 Unstimulated_S31 Unstimulated_S32
1 1 1 1
Unstimulated_S34 Unstimulated_S37 Unstimulated_S38 Unstimulated_S39
1 3 1 1
Unstimulated_S3 Unstimulated_S41 Unstimulated_S46 Unstimulated_S47
1 1 1 1
Unstimulated_S48 Unstimulated_S49 Unstimulated_S4 Unstimulated_S51
1 1 1 3
Unstimulated_S52 Unstimulated_S53 Unstimulated_S54 Unstimulated_S55
1 1 1 3
Unstimulated_S5 Unstimulated_S60 Unstimulated_S61 Unstimulated_S62
3 1 1 1
Unstimulated_S63 Unstimulated_S66 Unstimulated_S6 Unstimulated_S70
1 1 1 1
Unstimulated_S71 Unstimulated_S72 Unstimulated_S74 Unstimulated_S75
1 1 1 1
Unstimulated_S76 Unstimulated_S77 Unstimulated_S78 Unstimulated_S79
1 1 1 1
Unstimulated_S7 Unstimulated_S80 Unstimulated_S81 Unstimulated_S82
3 1 3 1
Unstimulated_S83 Unstimulated_S84 Unstimulated_S85 Unstimulated_S8
1 3 3 3
Unstimulated_S90 Unstimulated_S92 Unstimulated_S93 Unstimulated_S95
3 1 1 3
Unstimulated_S96 LPS_6h_S10 LPS_6h_S11 LPS_6h_S12
1 2 2 2
LPS_6h_S14 LPS_6h_S15 LPS_6h_S16 LPS_6h_S17
2 2 2 3
LPS_6h_S18 LPS_6h_S19 LPS_6h_S1 LPS_6h_S20
2 3 3 2
LPS_6h_S21 LPS_6h_S22 LPS_6h_S23 LPS_6h_S24
2 2 3 2
LPS_6h_S25 LPS_6h_S26 LPS_6h_S27 LPS_6h_S28
2 2 2 3
LPS_6h_S29 LPS_6h_S2 LPS_6h_S30 LPS_6h_S34
2 2 2 3
LPS_6h_S35 LPS_6h_S37 LPS_6h_S38 LPS_6h_S39
3 3 2 2
LPS_6h_S3 LPS_6h_S40 LPS_6h_S42 LPS_6h_S43
2 2 2 2
LPS_6h_S44 LPS_6h_S46 LPS_6h_S48 LPS_6h_S49
2 2 2 2
LPS_6h_S4 LPS_6h_S50 LPS_6h_S51 LPS_6h_S53
2 2 2 2
LPS_6h_S55 LPS_6h_S56 LPS_6h_S57 LPS_6h_S58
2 3 2 2
LPS_6h_S59 LPS_6h_S5 LPS_6h_S60 LPS_6h_S61
2 2 2 2
LPS_6h_S63 LPS_6h_S64 LPS_6h_S65 LPS_6h_S66
2 2 2 2
LPS_6h_S67 LPS_6h_S68 LPS_6h_S6 LPS_6h_S70
3 2 2 2
LPS_6h_S74 LPS_6h_S76 LPS_6h_S77 LPS_6h_S78
2 2 2 3
LPS_6h_S79 LPS_6h_S7 LPS_6h_S80 LPS_6h_S81
3 3 3 2
LPS_6h_S83 LPS_6h_S84 LPS_6h_S86 LPS_6h_S87
3 2 3 3
LPS_6h_S88 LPS_6h_S89 LPS_6h_S8 LPS_6h_S90
2 2 2 2
LPS_6h_S91 LPS_6h_S93 LPS_6h_S9
2 2 2
$clucenter
[,1] [,2] [,3] [,4] [,5]
[1,] -4.701208 -6.0001699 -0.2304098 0.6541102 0.1480404
[2,] 0.165610 4.8079024 1.4012641 -1.3636384 -0.2311658
[3,] 6.580446 -0.3347654 -2.3244674 1.6315513 0.2220892
TSCAN documentation built on Nov. 8, 2020, 5:13 p.m.
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Description Usage Arguments Details Value Author(s) References Examples
Description
Perform model-based clustering on expression values
Usage
1 | exprmclust(data, clusternum = 2:9, modelNames = "VVV", reduce = T)
|
Arguments
data |
The raw single_cell data, which is a numeric matrix or data.frame. Rows represent genes/features and columns represent single cells. |
clusternum |
An integer vector specifying all possible cluster numbers. The best cluster number will be picked using BIC. The minimum value should be two other |
modelNames |
model to be used in model-based clustering. By default "ellipsoidal, varying volume, shape, and orientation" is used. |
reduce |
Whether to perform the PCA on the expression data. |
Details
By default, this function first uses principal component analysis (PCA) to reduce dimensionality of original data. It then performs model-based clustering on the transformed expression values. A minimum-spanning-tree is constructed to link the cluster centers. The clustering results will be used for TSCAN ordering.
Value
if more than one cluster detected, a list containing
pcareduceres Numeric matrix containing the transformed expression values after PCA.
MSTtree igraph object which is the result of constructing MST.
clusterid A named vector specifying which cluster the cells belong to.
clucenter Numeric matrix of the cluster centers.
if only one cluster detected, a list containing
pcareduceres Numeric matrix containing the transformed expression values after PCA.
Author(s)
Zhicheng Ji, Hongkai Ji <zji4@zji4.edu>
References
Fraley, C., & Raftery, A. E. (2002). Model-based clustering, discriminant analysis, and density estimation. Journal of the American Statistical Association, 97(458), 611-631.
Examples
1 2 3 | data(lpsdata)
procdata <- preprocess(lpsdata)
exprmclust(procdata)
|
Example output
$pcareduceres
PC1 PC2 PC3 PC4 PC5
Unstimulated_S15 -4.92638297 -8.8529185 3.22733252 -2.530967511 -2.32018858
Unstimulated_S16 -6.53424105 2.7790245 -0.07747889 0.828806525 1.38991796
Unstimulated_S17 -4.37822709 -7.1209402 3.75669380 -1.880575370 -0.20894592
Unstimulated_S18 17.81566572 -4.9989393 5.89433717 0.498551168 0.37654921
Unstimulated_S23 4.63958402 -7.0623736 -0.16541202 1.884503386 -4.20403502
Unstimulated_S24 -5.11519374 -7.8997135 3.39796650 -3.705876957 -0.72953511
Unstimulated_S26 -5.61797356 -7.0595907 0.59760040 -0.830618710 -4.50418081
Unstimulated_S27 -16.00062653 -3.1312633 -0.71870458 1.113940481 -2.63587791
Unstimulated_S28 -7.66518422 -8.1902394 1.26091879 -2.130027451 -5.02037825
Unstimulated_S2 -7.01346590 -5.4934888 -1.37784833 1.466572277 4.56611985
Unstimulated_S31 -2.96507054 -3.5346277 -0.64206453 5.027971580 4.34014341
Unstimulated_S32 -2.61022408 -4.4616316 -1.10533938 0.434571738 4.00092481
Unstimulated_S34 -7.21965614 -4.0424538 -4.26155077 2.719748564 1.25508809
Unstimulated_S37 16.95835092 -5.4442503 5.10034345 1.603287505 -0.74659474
Unstimulated_S38 -11.22916670 -6.1224529 -1.21729258 -0.267079854 -1.73711700
Unstimulated_S39 -8.59346505 -6.6919448 0.07142350 0.549971696 1.19148416
Unstimulated_S3 -9.23322744 -3.5455576 -2.70894287 3.510278152 0.33302224
Unstimulated_S41 -2.38737204 -4.3388880 0.33955341 -2.645652053 10.18993650
Unstimulated_S46 -9.94907597 -4.8907295 -2.99509140 2.355224934 -1.41274142
Unstimulated_S47 -0.31980414 -5.5103084 -2.42844969 -0.440886113 1.38752524
Unstimulated_S48 -4.85597695 -6.6271405 -0.78445250 0.464599295 -6.21643850
Unstimulated_S49 -8.52832342 -7.0757567 -0.23212922 -1.232910859 -0.04610125
Unstimulated_S4 -1.67313748 -4.0589471 -1.76452598 0.711142629 -0.32216581
Unstimulated_S51 -6.05022337 -5.2222314 -9.85843013 0.032263153 1.44143540
Unstimulated_S52 -6.46344442 -5.8367555 0.48176676 3.486264194 0.60760780
Unstimulated_S53 -5.63582158 -3.3383028 -0.05760304 1.476669275 2.06340185
Unstimulated_S54 -0.84628345 -6.1867255 -5.47061553 0.209137854 -2.77552085
Unstimulated_S55 11.32263613 -7.0996464 3.91329851 0.307710659 0.50135403
Unstimulated_S5 0.35007434 -2.5303971 -0.69994892 -1.999123649 4.25006301
Unstimulated_S60 -8.38574750 -8.0671125 1.35441912 -1.448207726 -0.12567796
Unstimulated_S61 -8.97361103 -5.9023228 0.67988538 4.960491262 -1.11922858
Unstimulated_S62 -0.54632004 -7.5029215 2.73790070 -2.444717075 -2.65743490
Unstimulated_S63 -9.00060740 -4.8634030 -0.71524850 2.479860400 0.85320474
Unstimulated_S66 -6.96045778 -7.5509841 -0.45159996 0.734743680 -3.27054592
Unstimulated_S6 -3.71662075 -8.8188517 3.01350227 -1.390360390 -1.58972241
Unstimulated_S70 -6.31449548 -4.7744833 -2.53975012 0.903786856 0.39503315
Unstimulated_S71 -5.20887527 -6.7001860 -0.54456262 1.400067578 2.55685691
Unstimulated_S72 0.06053991 -3.8589266 -1.38365411 6.023712402 3.16191871
Unstimulated_S74 -1.21926738 -7.3115827 1.94698254 -1.931832975 -0.81712112
Unstimulated_S75 -2.42607251 -7.3594098 -0.78034205 -0.386519407 2.42879469
Unstimulated_S76 -1.14472728 -5.7108653 -3.92242548 1.964556081 4.86660657
Unstimulated_S77 -1.91827615 -4.9925797 2.10799225 1.867632369 5.41470502
Unstimulated_S78 -9.11918319 -6.6336481 0.50797940 -3.363948549 0.57338160
Unstimulated_S79 4.71193963 -7.0725255 0.84396847 -3.113547137 2.84111610
Unstimulated_S7 15.02717140 -3.1812831 -20.37863291 -0.195088580 -3.81874672
Unstimulated_S80 -6.16676261 -4.3178415 -4.46734816 4.330139633 3.38227484
Unstimulated_S81 14.68838230 -4.8070524 5.95065699 3.154664077 2.03882286
Unstimulated_S82 -11.18519764 -5.1538116 1.38012271 -0.546715656 -2.40312946
Unstimulated_S83 7.86295942 -8.4072488 1.72028689 -2.583946521 0.95359758
Unstimulated_S84 12.45244947 -7.3521724 6.14909952 -0.644095292 3.28545509
Unstimulated_S85 17.77990759 -5.6904395 6.05606450 0.429767132 -0.08124407
Unstimulated_S8 0.48902448 -3.1708219 -8.27172906 -2.165200456 5.66737518
Unstimulated_S90 -7.04643419 -0.6512254 -0.51337113 0.004834302 3.04673465
Unstimulated_S92 -1.76995672 -5.1857664 0.50378468 6.754768765 1.37016863
Unstimulated_S93 -6.32462213 -6.8513650 -2.26678468 4.944123477 -3.39052517
Unstimulated_S95 15.90686277 -5.9030986 4.81258389 1.951157858 -1.48268050
Unstimulated_S96 -0.52027265 -5.8988891 2.93362818 -0.119240743 -4.71252497
LPS_6h_S10 3.41059912 4.8026164 0.85047833 1.780947630 2.24298684
LPS_6h_S11 -7.00637482 3.0573865 3.72876703 -4.809485380 -1.01143877
LPS_6h_S12 -4.95769809 3.8583591 0.58008114 -4.185700849 1.35934163
LPS_6h_S14 -0.07711724 4.3329526 3.15257157 -3.697925011 -1.57703436
LPS_6h_S15 -5.99004365 8.5170997 -1.98223087 -1.112486090 1.72521617
LPS_6h_S16 3.25273365 6.9835752 -2.50910046 -3.692120681 6.61555100
LPS_6h_S17 0.16567101 6.5309662 -1.76889325 8.012914146 3.22717809
LPS_6h_S18 3.91965487 4.4234775 0.25898982 -1.530347415 2.43127779
LPS_6h_S19 12.97789991 -0.5000554 -25.02491519 -1.781497016 -2.97902446
LPS_6h_S1 -7.03719726 7.3093473 -0.77765713 5.999730375 -0.53922083
LPS_6h_S20 -2.46467845 6.5408224 0.65057878 -3.523567289 -1.27990616
LPS_6h_S21 1.70142697 3.9383284 3.90496265 -2.314455582 0.58854748
LPS_6h_S22 -1.07460769 5.2207599 1.27816169 1.794528181 1.68747620
LPS_6h_S23 3.10603550 2.8995015 0.87847805 7.187948276 -2.40253086
LPS_6h_S24 2.75229554 6.4929678 4.28272143 1.379262311 2.22417765
LPS_6h_S25 -5.69985751 5.4299413 1.84199357 -5.745291220 0.76557472
LPS_6h_S26 2.71074604 7.2928612 -3.27872848 0.033622977 -1.24818749
LPS_6h_S27 2.90714330 6.2549945 1.06585578 4.290505200 2.31777167
LPS_6h_S28 -7.89316669 9.1771654 -1.93875068 6.521291494 -0.78088003
LPS_6h_S29 -4.46761743 6.4024421 -1.46099382 -4.947388517 1.68933704
LPS_6h_S2 -3.70134238 4.2744424 2.18699427 -3.738905322 -2.27810844
LPS_6h_S30 -7.67553517 8.8862112 -0.65398568 -1.856313382 -0.16399463
LPS_6h_S34 -3.55916101 6.2490548 -0.35526252 5.723292570 -2.82033325
LPS_6h_S35 10.26778553 0.4457759 -14.57019357 -3.176624180 -1.57986357
LPS_6h_S37 6.02404404 2.3526877 0.41900957 6.941185763 3.36490615
LPS_6h_S38 -2.48745627 3.0196229 1.72433835 -5.331153776 -0.78868036
LPS_6h_S39 -3.33697250 5.0115097 -0.47750058 -5.776854123 -3.53991962
LPS_6h_S3 -0.83089207 5.5145241 -1.01037500 -5.480371858 3.06046678
LPS_6h_S40 -1.81799956 8.1188865 0.03516849 3.021234920 -3.55901507
LPS_6h_S42 -1.65975486 6.9848698 0.04203313 -2.974717382 -0.76239455
LPS_6h_S43 1.33163332 0.5941597 4.86591317 -4.589921089 -3.17288891
LPS_6h_S44 3.85282419 3.4886721 1.01623599 -3.487203830 3.33621142
LPS_6h_S46 9.05482707 -1.0029173 5.80845865 -0.571412817 -0.78218627
LPS_6h_S48 -6.31474913 8.4861760 -0.86959683 0.815151097 -1.84176737
LPS_6h_S49 2.16789966 7.4756361 1.63731632 4.872575491 0.91741317
LPS_6h_S4 4.12396129 4.3565106 5.66052678 3.763670326 -4.61965416
LPS_6h_S50 5.05947785 3.1909071 -1.11006714 0.842027130 1.73581780
LPS_6h_S51 -3.60413100 5.9866181 0.66599037 1.456320190 -1.55938739
LPS_6h_S53 -1.87468034 3.9185788 0.87665262 -3.886568930 3.06134877
LPS_6h_S55 3.05305193 3.6942515 4.64567130 -1.659525273 0.17408672
LPS_6h_S56 16.02356893 -2.4976457 6.04171666 -0.778524362 -2.12019207
LPS_6h_S57 1.40436177 3.6939251 1.82268348 2.165641163 -3.37870649
LPS_6h_S58 -1.06997022 4.6632060 -3.01245754 -6.021806669 2.54405641
LPS_6h_S59 4.83412988 0.8066678 3.08974965 -1.002525091 -0.25579360
LPS_6h_S5 6.72565183 3.6389907 5.81248089 2.443312906 -2.09759812
LPS_6h_S60 8.58558030 0.3053119 5.96519081 0.754855349 0.98161175
LPS_6h_S61 8.62886105 0.9265787 5.58806183 1.165773221 -2.88207983
LPS_6h_S63 -3.71412623 6.4200202 0.15583612 1.784154397 1.78659200
LPS_6h_S64 3.70134435 5.2299460 1.10664240 3.591449839 -3.97923918
LPS_6h_S65 5.39827669 3.2897982 -2.30315801 -3.283495666 0.48639437
LPS_6h_S66 2.72151929 1.0535344 1.93643449 -8.168103819 3.23690978
LPS_6h_S67 13.72681695 0.1066333 -14.98690823 -0.121052195 -3.67368564
LPS_6h_S68 -4.29003096 6.2523365 3.01941856 -1.582325433 2.52132017
LPS_6h_S6 4.65411117 4.1693852 -1.97612448 -0.511589227 -3.11966973
LPS_6h_S70 1.65116754 3.5729276 6.06804155 -0.470158640 0.96624273
LPS_6h_S74 -0.03292703 1.9839559 3.27426863 -5.816737301 -1.17881452
LPS_6h_S76 -2.99857718 6.1842686 1.21836077 -4.259185554 1.04919203
LPS_6h_S77 4.71109312 6.8728790 -1.72215350 3.925529129 -4.45211994
LPS_6h_S78 12.97375958 -0.1385897 -14.76922619 -4.623364748 -2.15527185
LPS_6h_S79 14.81506369 -2.1037154 0.94989966 -2.204786844 -0.75277072
LPS_6h_S7 4.12414975 0.7361231 4.93784192 4.797098269 -2.78452929
LPS_6h_S80 -11.32182828 5.7084215 -2.80129888 4.149089105 -0.03603544
LPS_6h_S81 -1.27659653 1.1660312 1.41473961 -6.802943862 -5.72519432
LPS_6h_S83 16.36402421 -1.6575890 6.21153834 1.427235737 -0.73814919
LPS_6h_S84 -1.83424737 6.3887328 1.35240135 2.220242728 -4.49141816
LPS_6h_S86 6.56470875 4.0209304 -5.36589766 1.891070782 2.41680209
LPS_6h_S87 6.93158472 4.5905606 -4.89029618 5.173998039 5.14783421
LPS_6h_S88 -9.68164837 6.6423318 -1.42270777 -1.702127235 -3.04629747
LPS_6h_S89 2.65038377 8.6424984 -0.13397975 3.829378276 1.11653735
LPS_6h_S8 -3.68096328 4.3332544 1.53220666 -6.333910685 2.89330302
LPS_6h_S90 -8.58848657 9.5353756 0.65084652 -1.374325026 -1.21007512
LPS_6h_S91 9.01267053 0.5864734 1.08695356 -6.216677798 1.57159708
LPS_6h_S93 -6.55617226 4.9763087 4.31312777 -1.008142282 -5.76542630
LPS_6h_S9 4.22759613 7.1684539 3.62730613 5.808200530 1.50418649
$MSTtree
IGRAPH 37b136c UNW- 3 2 --
+ attr: name (v/c), weight (e/n)
+ edges from 37b136c (vertex names):
[1] 1--2 2--3
$clusterid
Unstimulated_S15 Unstimulated_S16 Unstimulated_S17 Unstimulated_S18
1 3 1 3
Unstimulated_S23 Unstimulated_S24 Unstimulated_S26 Unstimulated_S27
1 1 1 1
Unstimulated_S28 Unstimulated_S2 Unstimulated_S31 Unstimulated_S32
1 1 1 1
Unstimulated_S34 Unstimulated_S37 Unstimulated_S38 Unstimulated_S39
1 3 1 1
Unstimulated_S3 Unstimulated_S41 Unstimulated_S46 Unstimulated_S47
1 1 1 1
Unstimulated_S48 Unstimulated_S49 Unstimulated_S4 Unstimulated_S51
1 1 1 3
Unstimulated_S52 Unstimulated_S53 Unstimulated_S54 Unstimulated_S55
1 1 1 3
Unstimulated_S5 Unstimulated_S60 Unstimulated_S61 Unstimulated_S62
3 1 1 1
Unstimulated_S63 Unstimulated_S66 Unstimulated_S6 Unstimulated_S70
1 1 1 1
Unstimulated_S71 Unstimulated_S72 Unstimulated_S74 Unstimulated_S75
1 1 1 1
Unstimulated_S76 Unstimulated_S77 Unstimulated_S78 Unstimulated_S79
1 1 1 1
Unstimulated_S7 Unstimulated_S80 Unstimulated_S81 Unstimulated_S82
3 1 3 1
Unstimulated_S83 Unstimulated_S84 Unstimulated_S85 Unstimulated_S8
1 3 3 3
Unstimulated_S90 Unstimulated_S92 Unstimulated_S93 Unstimulated_S95
3 1 1 3
Unstimulated_S96 LPS_6h_S10 LPS_6h_S11 LPS_6h_S12
1 2 2 2
LPS_6h_S14 LPS_6h_S15 LPS_6h_S16 LPS_6h_S17
2 2 2 3
LPS_6h_S18 LPS_6h_S19 LPS_6h_S1 LPS_6h_S20
2 3 3 2
LPS_6h_S21 LPS_6h_S22 LPS_6h_S23 LPS_6h_S24
2 2 3 2
LPS_6h_S25 LPS_6h_S26 LPS_6h_S27 LPS_6h_S28
2 2 2 3
LPS_6h_S29 LPS_6h_S2 LPS_6h_S30 LPS_6h_S34
2 2 2 3
LPS_6h_S35 LPS_6h_S37 LPS_6h_S38 LPS_6h_S39
3 3 2 2
LPS_6h_S3 LPS_6h_S40 LPS_6h_S42 LPS_6h_S43
2 2 2 2
LPS_6h_S44 LPS_6h_S46 LPS_6h_S48 LPS_6h_S49
2 2 2 2
LPS_6h_S4 LPS_6h_S50 LPS_6h_S51 LPS_6h_S53
2 2 2 2
LPS_6h_S55 LPS_6h_S56 LPS_6h_S57 LPS_6h_S58
2 3 2 2
LPS_6h_S59 LPS_6h_S5 LPS_6h_S60 LPS_6h_S61
2 2 2 2
LPS_6h_S63 LPS_6h_S64 LPS_6h_S65 LPS_6h_S66
2 2 2 2
LPS_6h_S67 LPS_6h_S68 LPS_6h_S6 LPS_6h_S70
3 2 2 2
LPS_6h_S74 LPS_6h_S76 LPS_6h_S77 LPS_6h_S78
2 2 2 3
LPS_6h_S79 LPS_6h_S7 LPS_6h_S80 LPS_6h_S81
3 3 3 2
LPS_6h_S83 LPS_6h_S84 LPS_6h_S86 LPS_6h_S87
3 2 3 3
LPS_6h_S88 LPS_6h_S89 LPS_6h_S8 LPS_6h_S90
2 2 2 2
LPS_6h_S91 LPS_6h_S93 LPS_6h_S9
2 2 2
$clucenter
[,1] [,2] [,3] [,4] [,5]
[1,] -4.701208 -6.0001699 -0.2304098 0.6541102 0.1480404
[2,] 0.165610 4.8079024 1.4012641 -1.3636384 -0.2311658
[3,] 6.580446 -0.3347654 -2.3244674 1.6315513 0.2220892
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