kmeans.run: Multiple runs of K-means analysis
In bios2mds: From Biological Sequences to Multidimensional Scaling
Description
Usage
Arguments
Details
Value
Note
Author(s)
Examples
Description
Performs multiple runs of K-means clustering and analyzes data.
Usage
1
2
kmeans.run(mat, nb.clus = 2, nb.run = 1000, iter.max = 10000,
method = "euclidean")
Arguments
mat
a numeric matrix representing the coordinates of the elements after metric MDS analysis.
nb.clus
a numeric value indicating the number of clusters. Default is 2.
nb.run
a numeric value indicating the number of runs. Default is 1000.
iter.max
a numeric value indicating the maximum number of iterations for K-means. Default is 10000.
method
a string of characters to determine the distance to be used. This should be one of "euclidean", "maximum",
"manhattan", "canberra", "binary", "pearson", "correlation", "spearman" or "kendall". Default is "euclidean".
Details
The aim of K-means clustering is the partition of elements into a user-provided number of clusters. Several runs of K-means analysis on the same data may return different cluster assignments because the K-means procedure attributes random initial centroids for each run. The robustness of an assignment depends on its reproducibility.
The function matchClasses from the e1071 package is used to compare the cluster assignments of the different runs and returns a score of agreement between them. The most frequent clustering solution is selected and used as a reference to assess the reproducibility of the analysis.
kmeans.run returns two lists. In either list, the clusters refer to those observed in the most frequent solution. The first list provides, for each element, the relative ratio of its assignment to each cluster in the different runs. The second list provides, for each cluster, the list of the assigned elements along with the relative assignment to this cluster in the different runs.
Value
A object of class 'kmean', which is a named list of two elements
elements
a named list of elements with the relative assignment of each element to each cluster.
clusters
a named list of clusters with the elements assigned to this cluster in the most frequent solution and their relative assignment to this cluster in multiple runs.
Note
During the K-means procedure, an empty cluster can be obtained if no objects are allocated to the
cluster. In kmeans.run, runs with empty clusters are discarded.
kmeans.run requires Kmeans and matchClasses functions from amap
and e1071 packages, respectively.
Author(s)
Julien Pele
Examples
1
2
3
4
5
6
# Clustering human GPCRs in 4 groups with 100 runs of K-means
data(gpcr)
coord <- gpcr$mmds$sapiens.active$coord
kmeans.run1 <- kmeans.run(coord, nb.clus = 4, nb.run = 100)
kmeans.run1$clusters
kmeans.run1$elements
Example output
Loading required package: amap
Loading required package: e1071
Loading required package: scales
Loading required package: cluster
Loading required package: rgl
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE
3: .onUnload failed in unloadNamespace() for 'rgl', details:
call: fun(...)
error: object 'rgl_quit' not found
$`1`
GPR82_HUMAN GP152_HUMAN RGR_HUMAN FSHR_HUMAN LSHR_HUMAN TSHR_HUMAN
100 99 88 88 88 88
LGR4_HUMAN LGR5_HUMAN LGR6_HUMAN RXFP1_HUMAN PD2R_HUMAN PE2R1_HUMAN
88 88 88 52 88 88
PE2R2_HUMAN PE2R3_HUMAN PE2R4_HUMAN PF2R_HUMAN PI2R_HUMAN TA2R_HUMAN
88 88 88 88 88 88
MAS_HUMAN MRGRD_HUMAN MRGRF_HUMAN MAS1L_HUMAN MRGRE_HUMAN MRGRG_HUMAN
99 99 99 99 99 99
MRGX1_HUMAN MRGX2_HUMAN MRGX3_HUMAN MRGX4_HUMAN ACTHR_HUMAN MC5R_HUMAN
99 99 99 99 71 52
MSHR_HUMAN GP119_HUMAN GPR12_HUMAN GPR3_HUMAN GPR6_HUMAN S1PR1_HUMAN
88 52 88 88 88 88
S1PR2_HUMAN S1PR3_HUMAN S1PR4_HUMAN S1PR5_HUMAN CNR1_HUMAN CNR2_HUMAN
88 88 88 88 88 88
LPAR1_HUMAN LPAR2_HUMAN LPAR3_HUMAN GP148_HUMAN GP150_HUMAN GP160_HUMAN
88 88 88 88 88 88
GPBAR_HUMAN GPR26_HUMAN GPR62_HUMAN GPR75_HUMAN GPR78_HUMAN GPR88_HUMAN
88 88 60 88 88 52
$`2`
MC3R_HUMAN MC4R_HUMAN AA1R_HUMAN AA2AR_HUMAN AA2BR_HUMAN AA3R_HUMAN
100 100 100 100 100 100
5HT1A_HUMAN 5HT1B_HUMAN 5HT1D_HUMAN 5HT1E_HUMAN 5HT1F_HUMAN 5HT2A_HUMAN
100 100 100 100 100 100
5HT2B_HUMAN 5HT2C_HUMAN 5HT4R_HUMAN 5HT5A_HUMAN 5HT6R_HUMAN 5HT7R_HUMAN
100 100 100 100 100 100
ACM1_HUMAN ACM2_HUMAN ACM3_HUMAN ACM4_HUMAN ACM5_HUMAN ADA1A_HUMAN
100 100 100 100 100 100
ADA1B_HUMAN ADA1D_HUMAN ADA2A_HUMAN ADA2B_HUMAN ADA2C_HUMAN ADRB1_HUMAN
100 100 100 100 100 100
ADRB2_HUMAN ADRB3_HUMAN DRD1_HUMAN DRD2_HUMAN DRD3_HUMAN DRD4_HUMAN
100 100 100 100 100 100
DRD5_HUMAN HRH1_HUMAN HRH2_HUMAN HRH3_HUMAN HRH4_HUMAN TAAR1_HUMAN
100 100 100 100 100 100
TAAR2_HUMAN TAAR3_HUMAN TAAR5_HUMAN TAAR6_HUMAN TAAR8_HUMAN TAAR9_HUMAN
100 100 100 100 100 100
$`3`
LT4R1_HUMAN LT4R2_HUMAN MCHR1_HUMAN UR2R_HUMAN BRS3_HUMAN CCKAR_HUMAN
100 100 100 100 100 100
EDNRA_HUMAN EDNRB_HUMAN ETBR2_HUMAN GALR1_HUMAN GALR2_HUMAN GALR3_HUMAN
100 100 100 100 100 100
GASR_HUMAN GHSR_HUMAN GNRHR_HUMAN GNRR2_HUMAN GP101_HUMAN GP135_HUMAN
100 100 100 100 100 100
GP151_HUMAN GP173_HUMAN GP176_HUMAN GPR19_HUMAN GPR27_HUMAN GPR37_HUMAN
100 100 100 100 100 100
GPR39_HUMAN GPR83_HUMAN GPR84_HUMAN GPR85_HUMAN GRPR_HUMAN KISSR_HUMAN
100 100 100 100 100 100
MTLR_HUMAN NK1R_HUMAN NK2R_HUMAN NK3R_HUMAN NMBR_HUMAN NMUR1_HUMAN
100 100 100 100 100 100
NMUR2_HUMAN NPFF1_HUMAN NPFF2_HUMAN NPSR1_HUMAN NPY1R_HUMAN NPY2R_HUMAN
100 100 100 100 100 100
NPY4R_HUMAN NPY5R_HUMAN NTR1_HUMAN NTR2_HUMAN OX1R_HUMAN OX2R_HUMAN
100 100 100 100 100 100
OXYR_HUMAN PKR1_HUMAN PKR2_HUMAN PRLHR_HUMAN QRFPR_HUMAN TRFR_HUMAN
100 100 100 100 100 100
V1AR_HUMAN V1BR_HUMAN V2R_HUMAN MTR1A_HUMAN MTR1B_HUMAN MTR1L_HUMAN
100 100 100 100 100 100
OPN3_HUMAN OPN4_HUMAN OPN5_HUMAN OPSB_HUMAN OPSD_HUMAN OPSR_HUMAN
100 100 100 100 100 100
OPSX_HUMAN RXFP2_HUMAN GP120_HUMAN GP139_HUMAN GP142_HUMAN GP146_HUMAN
100 100 100 100 100 100
GP161_HUMAN GPR21_HUMAN GPR22_HUMAN GPR45_HUMAN GPR52_HUMAN GPR61_HUMAN
100 100 100 100 100 100
GPR63_HUMAN Q5KU14_HUMAN
100 100
$`4`
CLTR1_HUMAN CLTR2_HUMAN FFAR1_HUMAN FFAR2_HUMAN FFAR3_HUMAN GP132_HUMAN
99 99 88 88 88 88
GP141_HUMAN GP171_HUMAN GP174_HUMAN GP183_HUMAN GPR17_HUMAN GPR18_HUMAN
88 88 88 99 89 88
GPR20_HUMAN GPR31_HUMAN GPR34_HUMAN GPR35_HUMAN GPR4_HUMAN GPR55_HUMAN
88 88 88 88 88 88
GPR81_HUMAN GPR87_HUMAN LPAR4_HUMAN LPAR5_HUMAN NIAR1_HUMAN OGR1_HUMAN
88 88 99 88 88 88
OXER1_HUMAN OXGR1_HUMAN P2RY1_HUMAN P2RY2_HUMAN P2RY4_HUMAN P2RY5_HUMAN
88 100 99 88 88 99
P2RY6_HUMAN P2RY8_HUMAN P2Y10_HUMAN P2Y11_HUMAN P2Y12_HUMAN P2Y13_HUMAN
99 88 88 89 88 88
P2Y14_HUMAN PAR1_HUMAN PAR2_HUMAN PAR3_HUMAN PAR4_HUMAN PSYR_HUMAN
88 88 88 88 88 88
PTAFR_HUMAN Q5KU21_HUMAN SUCR1_HUMAN AGTR1_HUMAN AGTR2_HUMAN APJ_HUMAN
88 88 100 100 100 100
BKRB1_HUMAN BKRB2_HUMAN C3AR_HUMAN C5ARL_HUMAN C5AR_HUMAN CCBP2_HUMAN
100 100 92 89 91 100
CCR10_HUMAN CCR1_HUMAN CCR2_HUMAN CCR3_HUMAN CCR4_HUMAN CCR5_HUMAN
100 100 100 100 100 100
CCR6_HUMAN CCR7_HUMAN CCR8_HUMAN CCR9_HUMAN CCRL1_HUMAN CCRL2_HUMAN
100 100 100 100 100 100
CML1_HUMAN CX3C1_HUMAN CXCR1_HUMAN CXCR2_HUMAN CXCR3_HUMAN CXCR4_HUMAN
100 100 100 100 100 100
CXCR5_HUMAN CXCR6_HUMAN CXCR7_HUMAN FPR1_HUMAN FPR2_HUMAN FPR3_HUMAN
100 100 100 100 100 100
GP182_HUMAN GPER_HUMAN GPR15_HUMAN GPR1_HUMAN GPR25_HUMAN GPR32_HUMAN
100 100 100 100 100 88
GPR33_HUMAN GPR44_HUMAN RL3R1_HUMAN RL3R2_HUMAN XCR1_HUMAN MCHR2_HUMAN
100 88 100 100 100 100
NPBW1_HUMAN NPBW2_HUMAN OPRD_HUMAN OPRK_HUMAN OPRM_HUMAN OPRX_HUMAN
100 100 100 100 100 100
SSR1_HUMAN SSR2_HUMAN SSR3_HUMAN SSR4_HUMAN SSR5_HUMAN
100 100 100 100 100
$CLTR1_HUMAN
1 2 3 4
1 0 0 99
$CLTR2_HUMAN
1 2 3 4
1 0 0 99
$FFAR1_HUMAN
1 2 3 4
12 0 0 88
$FFAR2_HUMAN
1 2 3 4
12 0 0 88
$FFAR3_HUMAN
1 2 3 4
12 0 0 88
$GP132_HUMAN
1 2 3 4
12 0 0 88
$GP141_HUMAN
1 2 3 4
12 0 0 88
$GP171_HUMAN
1 2 3 4
12 0 0 88
$GP174_HUMAN
1 2 3 4
12 0 0 88
$GP183_HUMAN
1 2 3 4
1 0 0 99
$GPR17_HUMAN
1 2 3 4
11 0 0 89
$GPR18_HUMAN
1 2 3 4
12 0 0 88
$GPR20_HUMAN
1 2 3 4
12 0 0 88
$GPR31_HUMAN
1 2 3 4
12 0 0 88
$GPR34_HUMAN
1 2 3 4
12 0 0 88
$GPR35_HUMAN
1 2 3 4
12 0 0 88
$GPR4_HUMAN
1 2 3 4
12 0 0 88
$GPR55_HUMAN
1 2 3 4
12 0 0 88
$GPR81_HUMAN
1 2 3 4
12 0 0 88
$GPR82_HUMAN
1 2 3 4
100 0 0 0
$GPR87_HUMAN
1 2 3 4
12 0 0 88
$LPAR4_HUMAN
1 2 3 4
1 0 0 99
$LPAR5_HUMAN
1 2 3 4
12 0 0 88
$NIAR1_HUMAN
1 2 3 4
12 0 0 88
$OGR1_HUMAN
1 2 3 4
12 0 0 88
$OXER1_HUMAN
1 2 3 4
12 0 0 88
$OXGR1_HUMAN
1 2 3 4
0 0 0 100
$P2RY1_HUMAN
1 2 3 4
1 0 0 99
$P2RY2_HUMAN
1 2 3 4
12 0 0 88
$P2RY4_HUMAN
1 2 3 4
12 0 0 88
$P2RY5_HUMAN
1 2 3 4
1 0 0 99
$P2RY6_HUMAN
1 2 3 4
1 0 0 99
$P2RY8_HUMAN
1 2 3 4
12 0 0 88
$P2Y10_HUMAN
1 2 3 4
12 0 0 88
$P2Y11_HUMAN
1 2 3 4
11 0 0 89
$P2Y12_HUMAN
1 2 3 4
12 0 0 88
$P2Y13_HUMAN
1 2 3 4
12 0 0 88
$P2Y14_HUMAN
1 2 3 4
12 0 0 88
$PAR1_HUMAN
1 2 3 4
12 0 0 88
$PAR2_HUMAN
1 2 3 4
12 0 0 88
$PAR3_HUMAN
1 2 3 4
12 0 0 88
$PAR4_HUMAN
1 2 3 4
12 0 0 88
$PSYR_HUMAN
1 2 3 4
12 0 0 88
$PTAFR_HUMAN
1 2 3 4
12 0 0 88
$Q5KU21_HUMAN
1 2 3 4
12 0 0 88
$SUCR1_HUMAN
1 2 3 4
0 0 0 100
$AGTR1_HUMAN
1 2 3 4
0 0 0 100
$AGTR2_HUMAN
1 2 3 4
0 0 0 100
$APJ_HUMAN
1 2 3 4
0 0 0 100
$BKRB1_HUMAN
1 2 3 4
0 0 0 100
$BKRB2_HUMAN
1 2 3 4
0 0 0 100
$C3AR_HUMAN
1 2 3 4
8 0 0 92
$C5ARL_HUMAN
1 2 3 4
11 0 0 89
$C5AR_HUMAN
1 2 3 4
9 0 0 91
$CCBP2_HUMAN
1 2 3 4
0 0 0 100
$CCR10_HUMAN
1 2 3 4
0 0 0 100
$CCR1_HUMAN
1 2 3 4
0 0 0 100
$CCR2_HUMAN
1 2 3 4
0 0 0 100
$CCR3_HUMAN
1 2 3 4
0 0 0 100
$CCR4_HUMAN
1 2 3 4
0 0 0 100
$CCR5_HUMAN
1 2 3 4
0 0 0 100
$CCR6_HUMAN
1 2 3 4
0 0 0 100
$CCR7_HUMAN
1 2 3 4
0 0 0 100
$CCR8_HUMAN
1 2 3 4
0 0 0 100
$CCR9_HUMAN
1 2 3 4
0 0 0 100
$CCRL1_HUMAN
1 2 3 4
0 0 0 100
$CCRL2_HUMAN
1 2 3 4
0 0 0 100
$CML1_HUMAN
1 2 3 4
0 0 0 100
$CX3C1_HUMAN
1 2 3 4
0 0 0 100
$CXCR1_HUMAN
1 2 3 4
0 0 0 100
$CXCR2_HUMAN
1 2 3 4
0 0 0 100
$CXCR3_HUMAN
1 2 3 4
0 0 0 100
$CXCR4_HUMAN
1 2 3 4
0 0 0 100
$CXCR5_HUMAN
1 2 3 4
0 0 0 100
$CXCR6_HUMAN
1 2 3 4
0 0 0 100
$CXCR7_HUMAN
1 2 3 4
0 0 0 100
$FPR1_HUMAN
1 2 3 4
0 0 0 100
$FPR2_HUMAN
1 2 3 4
0 0 0 100
$FPR3_HUMAN
1 2 3 4
0 0 0 100
$GP152_HUMAN
1 2 3 4
99 0 1 0
$GP182_HUMAN
1 2 3 4
0 0 0 100
$GPER_HUMAN
1 2 3 4
0 0 0 100
$GPR15_HUMAN
1 2 3 4
0 0 0 100
$GPR1_HUMAN
1 2 3 4
0 0 0 100
$GPR25_HUMAN
1 2 3 4
0 0 0 100
$GPR32_HUMAN
1 2 3 4
12 0 0 88
$GPR33_HUMAN
1 2 3 4
0 0 0 100
$GPR44_HUMAN
1 2 3 4
12 0 0 88
$LT4R1_HUMAN
1 2 3 4
0 0 100 0
$LT4R2_HUMAN
1 2 3 4
0 0 100 0
$RL3R1_HUMAN
1 2 3 4
0 0 0 100
$RL3R2_HUMAN
1 2 3 4
0 0 0 100
$XCR1_HUMAN
1 2 3 4
0 0 0 100
$MCHR1_HUMAN
1 2 3 4
0 0 100 0
$MCHR2_HUMAN
1 2 3 4
0 0 0 100
$NPBW1_HUMAN
1 2 3 4
0 0 0 100
$NPBW2_HUMAN
1 2 3 4
0 0 0 100
$OPRD_HUMAN
1 2 3 4
0 0 0 100
$OPRK_HUMAN
1 2 3 4
0 0 0 100
$OPRM_HUMAN
1 2 3 4
0 0 0 100
$OPRX_HUMAN
1 2 3 4
0 0 0 100
$SSR1_HUMAN
1 2 3 4
0 0 0 100
$SSR2_HUMAN
1 2 3 4
0 0 0 100
$SSR3_HUMAN
1 2 3 4
0 0 0 100
$SSR4_HUMAN
1 2 3 4
0 0 0 100
$SSR5_HUMAN
1 2 3 4
0 0 0 100
$UR2R_HUMAN
1 2 3 4
0 0 100 0
$BRS3_HUMAN
1 2 3 4
0 0 100 0
$CCKAR_HUMAN
1 2 3 4
0 0 100 0
$EDNRA_HUMAN
1 2 3 4
0 0 100 0
$EDNRB_HUMAN
1 2 3 4
0 0 100 0
$ETBR2_HUMAN
1 2 3 4
0 0 100 0
$GALR1_HUMAN
1 2 3 4
0 0 100 0
$GALR2_HUMAN
1 2 3 4
0 0 100 0
$GALR3_HUMAN
1 2 3 4
0 0 100 0
$GASR_HUMAN
1 2 3 4
0 0 100 0
$GHSR_HUMAN
1 2 3 4
0 0 100 0
$GNRHR_HUMAN
1 2 3 4
0 0 100 0
$GNRR2_HUMAN
1 2 3 4
0 0 100 0
$GP101_HUMAN
1 2 3 4
0 0 100 0
$GP135_HUMAN
1 2 3 4
0 0 100 0
$GP151_HUMAN
1 2 3 4
0 0 100 0
$GP173_HUMAN
1 2 3 4
0 0 100 0
$GP176_HUMAN
1 2 3 4
0 0 100 0
$GPR19_HUMAN
1 2 3 4
0 0 100 0
$GPR27_HUMAN
1 2 3 4
0 0 100 0
$GPR37_HUMAN
1 2 3 4
0 0 100 0
$GPR39_HUMAN
1 2 3 4
0 0 100 0
$GPR83_HUMAN
1 2 3 4
0 0 100 0
$GPR84_HUMAN
1 2 3 4
0 0 100 0
$GPR85_HUMAN
1 2 3 4
0 0 100 0
$GRPR_HUMAN
1 2 3 4
0 0 100 0
$KISSR_HUMAN
1 2 3 4
0 0 100 0
$MTLR_HUMAN
1 2 3 4
0 0 100 0
$NK1R_HUMAN
1 2 3 4
0 0 100 0
$NK2R_HUMAN
1 2 3 4
0 0 100 0
$NK3R_HUMAN
1 2 3 4
0 0 100 0
$NMBR_HUMAN
1 2 3 4
0 0 100 0
$NMUR1_HUMAN
1 2 3 4
0 0 100 0
$NMUR2_HUMAN
1 2 3 4
0 0 100 0
$NPFF1_HUMAN
1 2 3 4
0 0 100 0
$NPFF2_HUMAN
1 2 3 4
0 0 100 0
$NPSR1_HUMAN
1 2 3 4
0 0 100 0
$NPY1R_HUMAN
1 2 3 4
0 0 100 0
$NPY2R_HUMAN
1 2 3 4
0 0 100 0
$NPY4R_HUMAN
1 2 3 4
0 0 100 0
$NPY5R_HUMAN
1 2 3 4
0 0 100 0
$NTR1_HUMAN
1 2 3 4
0 0 100 0
$NTR2_HUMAN
1 2 3 4
0 0 100 0
$OX1R_HUMAN
1 2 3 4
0 0 100 0
$OX2R_HUMAN
1 2 3 4
0 0 100 0
$OXYR_HUMAN
1 2 3 4
0 0 100 0
$PKR1_HUMAN
1 2 3 4
0 0 100 0
$PKR2_HUMAN
1 2 3 4
0 0 100 0
$PRLHR_HUMAN
1 2 3 4
0 0 100 0
$QRFPR_HUMAN
1 2 3 4
0 0 100 0
$TRFR_HUMAN
1 2 3 4
0 0 100 0
$V1AR_HUMAN
1 2 3 4
0 0 100 0
$V1BR_HUMAN
1 2 3 4
0 0 100 0
$V2R_HUMAN
1 2 3 4
0 0 100 0
$MTR1A_HUMAN
1 2 3 4
0 0 100 0
$MTR1B_HUMAN
1 2 3 4
0 0 100 0
$MTR1L_HUMAN
1 2 3 4
0 0 100 0
$OPN3_HUMAN
1 2 3 4
0 0 100 0
$OPN4_HUMAN
1 2 3 4
0 0 100 0
$OPN5_HUMAN
1 2 3 4
0 0 100 0
$OPSB_HUMAN
1 2 3 4
0 0 100 0
$OPSD_HUMAN
1 2 3 4
0 0 100 0
$OPSR_HUMAN
1 2 3 4
0 0 100 0
$OPSX_HUMAN
1 2 3 4
0 0 100 0
$RGR_HUMAN
1 2 3 4
88 0 12 0
$FSHR_HUMAN
1 2 3 4
88 0 12 0
$LSHR_HUMAN
1 2 3 4
88 0 12 0
$TSHR_HUMAN
1 2 3 4
88 0 12 0
$LGR4_HUMAN
1 2 3 4
88 0 12 0
$LGR5_HUMAN
1 2 3 4
88 0 12 0
$LGR6_HUMAN
1 2 3 4
88 0 12 0
$RXFP1_HUMAN
1 2 3 4
52 0 48 0
$RXFP2_HUMAN
1 2 3 4
0 0 100 0
$PD2R_HUMAN
1 2 3 4
88 0 12 0
$PE2R1_HUMAN
1 2 3 4
88 0 12 0
$PE2R2_HUMAN
1 2 3 4
88 0 12 0
$PE2R3_HUMAN
1 2 3 4
88 0 12 0
$PE2R4_HUMAN
1 2 3 4
88 0 12 0
$PF2R_HUMAN
1 2 3 4
88 0 12 0
$PI2R_HUMAN
1 2 3 4
88 0 12 0
$TA2R_HUMAN
1 2 3 4
88 0 12 0
$MAS_HUMAN
1 2 3 4
99 0 1 0
$MRGRD_HUMAN
1 2 3 4
99 0 1 0
$MRGRF_HUMAN
1 2 3 4
99 0 1 0
$MAS1L_HUMAN
1 2 3 4
99 0 1 0
$MRGRE_HUMAN
1 2 3 4
99 0 1 0
$MRGRG_HUMAN
1 2 3 4
99 0 1 0
$MRGX1_HUMAN
1 2 3 4
99 0 1 0
$MRGX2_HUMAN
1 2 3 4
99 0 1 0
$MRGX3_HUMAN
1 2 3 4
99 0 1 0
$MRGX4_HUMAN
1 2 3 4
99 0 1 0
$ACTHR_HUMAN
1 2 3 4
71 29 0 0
$MC3R_HUMAN
1 2 3 4
0 100 0 0
$MC4R_HUMAN
1 2 3 4
0 100 0 0
$MC5R_HUMAN
1 2 3 4
52 48 0 0
$MSHR_HUMAN
1 2 3 4
88 12 0 0
$GP119_HUMAN
1 2 3 4
52 48 0 0
$GPR12_HUMAN
1 2 3 4
88 12 0 0
$GPR3_HUMAN
1 2 3 4
88 12 0 0
$GPR6_HUMAN
1 2 3 4
88 12 0 0
$S1PR1_HUMAN
1 2 3 4
88 12 0 0
$S1PR2_HUMAN
1 2 3 4
88 12 0 0
$S1PR3_HUMAN
1 2 3 4
88 12 0 0
$S1PR4_HUMAN
1 2 3 4
88 0 12 0
$S1PR5_HUMAN
1 2 3 4
88 0 12 0
$CNR1_HUMAN
1 2 3 4
88 12 0 0
$CNR2_HUMAN
1 2 3 4
88 12 0 0
$LPAR1_HUMAN
1 2 3 4
88 12 0 0
$LPAR2_HUMAN
1 2 3 4
88 11 1 0
$LPAR3_HUMAN
1 2 3 4
88 12 0 0
$AA1R_HUMAN
1 2 3 4
0 100 0 0
$AA2AR_HUMAN
1 2 3 4
0 100 0 0
$AA2BR_HUMAN
1 2 3 4
0 100 0 0
$AA3R_HUMAN
1 2 3 4
0 100 0 0
$`5HT1A_HUMAN`
1 2 3 4
0 100 0 0
$`5HT1B_HUMAN`
1 2 3 4
0 100 0 0
$`5HT1D_HUMAN`
1 2 3 4
0 100 0 0
$`5HT1E_HUMAN`
1 2 3 4
0 100 0 0
$`5HT1F_HUMAN`
1 2 3 4
0 100 0 0
$`5HT2A_HUMAN`
1 2 3 4
0 100 0 0
$`5HT2B_HUMAN`
1 2 3 4
0 100 0 0
$`5HT2C_HUMAN`
1 2 3 4
0 100 0 0
$`5HT4R_HUMAN`
1 2 3 4
0 100 0 0
$`5HT5A_HUMAN`
1 2 3 4
0 100 0 0
$`5HT6R_HUMAN`
1 2 3 4
0 100 0 0
$`5HT7R_HUMAN`
1 2 3 4
0 100 0 0
$ACM1_HUMAN
1 2 3 4
0 100 0 0
$ACM2_HUMAN
1 2 3 4
0 100 0 0
$ACM3_HUMAN
1 2 3 4
0 100 0 0
$ACM4_HUMAN
1 2 3 4
0 100 0 0
$ACM5_HUMAN
1 2 3 4
0 100 0 0
$ADA1A_HUMAN
1 2 3 4
0 100 0 0
$ADA1B_HUMAN
1 2 3 4
0 100 0 0
$ADA1D_HUMAN
1 2 3 4
0 100 0 0
$ADA2A_HUMAN
1 2 3 4
0 100 0 0
$ADA2B_HUMAN
1 2 3 4
0 100 0 0
$ADA2C_HUMAN
1 2 3 4
0 100 0 0
$ADRB1_HUMAN
1 2 3 4
0 100 0 0
$ADRB2_HUMAN
1 2 3 4
0 100 0 0
$ADRB3_HUMAN
1 2 3 4
0 100 0 0
$DRD1_HUMAN
1 2 3 4
0 100 0 0
$DRD2_HUMAN
1 2 3 4
0 100 0 0
$DRD3_HUMAN
1 2 3 4
0 100 0 0
$DRD4_HUMAN
1 2 3 4
0 100 0 0
$DRD5_HUMAN
1 2 3 4
0 100 0 0
$HRH1_HUMAN
1 2 3 4
0 100 0 0
$HRH2_HUMAN
1 2 3 4
0 100 0 0
$HRH3_HUMAN
1 2 3 4
0 100 0 0
$HRH4_HUMAN
1 2 3 4
0 100 0 0
$TAAR1_HUMAN
1 2 3 4
0 100 0 0
$TAAR2_HUMAN
1 2 3 4
0 100 0 0
$TAAR3_HUMAN
1 2 3 4
0 100 0 0
$TAAR5_HUMAN
1 2 3 4
0 100 0 0
$TAAR6_HUMAN
1 2 3 4
0 100 0 0
$TAAR8_HUMAN
1 2 3 4
0 100 0 0
$TAAR9_HUMAN
1 2 3 4
0 100 0 0
$GP120_HUMAN
1 2 3 4
0 0 100 0
$GP139_HUMAN
1 2 3 4
0 0 100 0
$GP142_HUMAN
1 2 3 4
0 0 100 0
$GP146_HUMAN
1 2 3 4
0 0 100 0
$GP148_HUMAN
1 2 3 4
88 0 12 0
$GP150_HUMAN
1 2 3 4
88 0 12 0
$GP160_HUMAN
1 2 3 4
88 0 12 0
$GP161_HUMAN
1 2 3 4
0 0 100 0
$GPBAR_HUMAN
1 2 3 4
88 0 12 0
$GPR21_HUMAN
1 2 3 4
0 0 100 0
$GPR22_HUMAN
1 2 3 4
0 0 100 0
$GPR26_HUMAN
1 2 3 4
88 0 12 0
$GPR45_HUMAN
1 2 3 4
0 0 100 0
$GPR52_HUMAN
1 2 3 4
0 0 100 0
$GPR61_HUMAN
1 2 3 4
0 0 100 0
$GPR62_HUMAN
1 2 3 4
60 0 40 0
$GPR63_HUMAN
1 2 3 4
0 0 100 0
$GPR75_HUMAN
1 2 3 4
88 0 12 0
$GPR78_HUMAN
1 2 3 4
88 0 12 0
$GPR88_HUMAN
1 2 3 4
52 0 48 0
$Q5KU14_HUMAN
1 2 3 4
0 0 100 0
bios2mds documentation built on April 14, 2020, 5:08 p.m.
R Package Documentation
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Description Usage Arguments Details Value Note Author(s) Examples
Description
Performs multiple runs of K-means clustering and analyzes data.
Usage
1 2 | kmeans.run(mat, nb.clus = 2, nb.run = 1000, iter.max = 10000,
method = "euclidean")
|
Arguments
mat |
a numeric matrix representing the coordinates of the elements after metric MDS analysis. |
nb.clus |
a numeric value indicating the number of clusters. Default is 2. |
nb.run |
a numeric value indicating the number of runs. Default is 1000. |
iter.max |
a numeric value indicating the maximum number of iterations for K-means. Default is 10000. |
method |
a string of characters to determine the distance to be used. This should be one of "euclidean", "maximum", "manhattan", "canberra", "binary", "pearson", "correlation", "spearman" or "kendall". Default is "euclidean". |
Details
The aim of K-means clustering is the partition of elements into a user-provided number of clusters. Several runs of K-means analysis on the same data may return different cluster assignments because the K-means procedure attributes random initial centroids for each run. The robustness of an assignment depends on its reproducibility.
The function matchClasses from the e1071 package is used to compare the cluster assignments of the different runs and returns a score of agreement between them. The most frequent clustering solution is selected and used as a reference to assess the reproducibility of the analysis.
kmeans.run returns two lists. In either list, the clusters refer to those observed in the most frequent solution. The first list provides, for each element, the relative ratio of its assignment to each cluster in the different runs. The second list provides, for each cluster, the list of the assigned elements along with the relative assignment to this cluster in the different runs.
Value
A object of class 'kmean', which is a named list of two elements
elements |
a named list of elements with the relative assignment of each element to each cluster. |
clusters |
a named list of clusters with the elements assigned to this cluster in the most frequent solution and their relative assignment to this cluster in multiple runs. |
Note
During the K-means procedure, an empty cluster can be obtained if no objects are allocated to the
cluster. In kmeans.run, runs with empty clusters are discarded.
kmeans.run requires Kmeans and matchClasses functions from amap
and e1071 packages, respectively.
Author(s)
Julien Pele
Examples
1 2 3 4 5 6 | # Clustering human GPCRs in 4 groups with 100 runs of K-means
data(gpcr)
coord <- gpcr$mmds$sapiens.active$coord
kmeans.run1 <- kmeans.run(coord, nb.clus = 4, nb.run = 100)
kmeans.run1$clusters
kmeans.run1$elements
|
Example output
Loading required package: amap
Loading required package: e1071
Loading required package: scales
Loading required package: cluster
Loading required package: rgl
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE
3: .onUnload failed in unloadNamespace() for 'rgl', details:
call: fun(...)
error: object 'rgl_quit' not found
$`1`
GPR82_HUMAN GP152_HUMAN RGR_HUMAN FSHR_HUMAN LSHR_HUMAN TSHR_HUMAN
100 99 88 88 88 88
LGR4_HUMAN LGR5_HUMAN LGR6_HUMAN RXFP1_HUMAN PD2R_HUMAN PE2R1_HUMAN
88 88 88 52 88 88
PE2R2_HUMAN PE2R3_HUMAN PE2R4_HUMAN PF2R_HUMAN PI2R_HUMAN TA2R_HUMAN
88 88 88 88 88 88
MAS_HUMAN MRGRD_HUMAN MRGRF_HUMAN MAS1L_HUMAN MRGRE_HUMAN MRGRG_HUMAN
99 99 99 99 99 99
MRGX1_HUMAN MRGX2_HUMAN MRGX3_HUMAN MRGX4_HUMAN ACTHR_HUMAN MC5R_HUMAN
99 99 99 99 71 52
MSHR_HUMAN GP119_HUMAN GPR12_HUMAN GPR3_HUMAN GPR6_HUMAN S1PR1_HUMAN
88 52 88 88 88 88
S1PR2_HUMAN S1PR3_HUMAN S1PR4_HUMAN S1PR5_HUMAN CNR1_HUMAN CNR2_HUMAN
88 88 88 88 88 88
LPAR1_HUMAN LPAR2_HUMAN LPAR3_HUMAN GP148_HUMAN GP150_HUMAN GP160_HUMAN
88 88 88 88 88 88
GPBAR_HUMAN GPR26_HUMAN GPR62_HUMAN GPR75_HUMAN GPR78_HUMAN GPR88_HUMAN
88 88 60 88 88 52
$`2`
MC3R_HUMAN MC4R_HUMAN AA1R_HUMAN AA2AR_HUMAN AA2BR_HUMAN AA3R_HUMAN
100 100 100 100 100 100
5HT1A_HUMAN 5HT1B_HUMAN 5HT1D_HUMAN 5HT1E_HUMAN 5HT1F_HUMAN 5HT2A_HUMAN
100 100 100 100 100 100
5HT2B_HUMAN 5HT2C_HUMAN 5HT4R_HUMAN 5HT5A_HUMAN 5HT6R_HUMAN 5HT7R_HUMAN
100 100 100 100 100 100
ACM1_HUMAN ACM2_HUMAN ACM3_HUMAN ACM4_HUMAN ACM5_HUMAN ADA1A_HUMAN
100 100 100 100 100 100
ADA1B_HUMAN ADA1D_HUMAN ADA2A_HUMAN ADA2B_HUMAN ADA2C_HUMAN ADRB1_HUMAN
100 100 100 100 100 100
ADRB2_HUMAN ADRB3_HUMAN DRD1_HUMAN DRD2_HUMAN DRD3_HUMAN DRD4_HUMAN
100 100 100 100 100 100
DRD5_HUMAN HRH1_HUMAN HRH2_HUMAN HRH3_HUMAN HRH4_HUMAN TAAR1_HUMAN
100 100 100 100 100 100
TAAR2_HUMAN TAAR3_HUMAN TAAR5_HUMAN TAAR6_HUMAN TAAR8_HUMAN TAAR9_HUMAN
100 100 100 100 100 100
$`3`
LT4R1_HUMAN LT4R2_HUMAN MCHR1_HUMAN UR2R_HUMAN BRS3_HUMAN CCKAR_HUMAN
100 100 100 100 100 100
EDNRA_HUMAN EDNRB_HUMAN ETBR2_HUMAN GALR1_HUMAN GALR2_HUMAN GALR3_HUMAN
100 100 100 100 100 100
GASR_HUMAN GHSR_HUMAN GNRHR_HUMAN GNRR2_HUMAN GP101_HUMAN GP135_HUMAN
100 100 100 100 100 100
GP151_HUMAN GP173_HUMAN GP176_HUMAN GPR19_HUMAN GPR27_HUMAN GPR37_HUMAN
100 100 100 100 100 100
GPR39_HUMAN GPR83_HUMAN GPR84_HUMAN GPR85_HUMAN GRPR_HUMAN KISSR_HUMAN
100 100 100 100 100 100
MTLR_HUMAN NK1R_HUMAN NK2R_HUMAN NK3R_HUMAN NMBR_HUMAN NMUR1_HUMAN
100 100 100 100 100 100
NMUR2_HUMAN NPFF1_HUMAN NPFF2_HUMAN NPSR1_HUMAN NPY1R_HUMAN NPY2R_HUMAN
100 100 100 100 100 100
NPY4R_HUMAN NPY5R_HUMAN NTR1_HUMAN NTR2_HUMAN OX1R_HUMAN OX2R_HUMAN
100 100 100 100 100 100
OXYR_HUMAN PKR1_HUMAN PKR2_HUMAN PRLHR_HUMAN QRFPR_HUMAN TRFR_HUMAN
100 100 100 100 100 100
V1AR_HUMAN V1BR_HUMAN V2R_HUMAN MTR1A_HUMAN MTR1B_HUMAN MTR1L_HUMAN
100 100 100 100 100 100
OPN3_HUMAN OPN4_HUMAN OPN5_HUMAN OPSB_HUMAN OPSD_HUMAN OPSR_HUMAN
100 100 100 100 100 100
OPSX_HUMAN RXFP2_HUMAN GP120_HUMAN GP139_HUMAN GP142_HUMAN GP146_HUMAN
100 100 100 100 100 100
GP161_HUMAN GPR21_HUMAN GPR22_HUMAN GPR45_HUMAN GPR52_HUMAN GPR61_HUMAN
100 100 100 100 100 100
GPR63_HUMAN Q5KU14_HUMAN
100 100
$`4`
CLTR1_HUMAN CLTR2_HUMAN FFAR1_HUMAN FFAR2_HUMAN FFAR3_HUMAN GP132_HUMAN
99 99 88 88 88 88
GP141_HUMAN GP171_HUMAN GP174_HUMAN GP183_HUMAN GPR17_HUMAN GPR18_HUMAN
88 88 88 99 89 88
GPR20_HUMAN GPR31_HUMAN GPR34_HUMAN GPR35_HUMAN GPR4_HUMAN GPR55_HUMAN
88 88 88 88 88 88
GPR81_HUMAN GPR87_HUMAN LPAR4_HUMAN LPAR5_HUMAN NIAR1_HUMAN OGR1_HUMAN
88 88 99 88 88 88
OXER1_HUMAN OXGR1_HUMAN P2RY1_HUMAN P2RY2_HUMAN P2RY4_HUMAN P2RY5_HUMAN
88 100 99 88 88 99
P2RY6_HUMAN P2RY8_HUMAN P2Y10_HUMAN P2Y11_HUMAN P2Y12_HUMAN P2Y13_HUMAN
99 88 88 89 88 88
P2Y14_HUMAN PAR1_HUMAN PAR2_HUMAN PAR3_HUMAN PAR4_HUMAN PSYR_HUMAN
88 88 88 88 88 88
PTAFR_HUMAN Q5KU21_HUMAN SUCR1_HUMAN AGTR1_HUMAN AGTR2_HUMAN APJ_HUMAN
88 88 100 100 100 100
BKRB1_HUMAN BKRB2_HUMAN C3AR_HUMAN C5ARL_HUMAN C5AR_HUMAN CCBP2_HUMAN
100 100 92 89 91 100
CCR10_HUMAN CCR1_HUMAN CCR2_HUMAN CCR3_HUMAN CCR4_HUMAN CCR5_HUMAN
100 100 100 100 100 100
CCR6_HUMAN CCR7_HUMAN CCR8_HUMAN CCR9_HUMAN CCRL1_HUMAN CCRL2_HUMAN
100 100 100 100 100 100
CML1_HUMAN CX3C1_HUMAN CXCR1_HUMAN CXCR2_HUMAN CXCR3_HUMAN CXCR4_HUMAN
100 100 100 100 100 100
CXCR5_HUMAN CXCR6_HUMAN CXCR7_HUMAN FPR1_HUMAN FPR2_HUMAN FPR3_HUMAN
100 100 100 100 100 100
GP182_HUMAN GPER_HUMAN GPR15_HUMAN GPR1_HUMAN GPR25_HUMAN GPR32_HUMAN
100 100 100 100 100 88
GPR33_HUMAN GPR44_HUMAN RL3R1_HUMAN RL3R2_HUMAN XCR1_HUMAN MCHR2_HUMAN
100 88 100 100 100 100
NPBW1_HUMAN NPBW2_HUMAN OPRD_HUMAN OPRK_HUMAN OPRM_HUMAN OPRX_HUMAN
100 100 100 100 100 100
SSR1_HUMAN SSR2_HUMAN SSR3_HUMAN SSR4_HUMAN SSR5_HUMAN
100 100 100 100 100
$CLTR1_HUMAN
1 2 3 4
1 0 0 99
$CLTR2_HUMAN
1 2 3 4
1 0 0 99
$FFAR1_HUMAN
1 2 3 4
12 0 0 88
$FFAR2_HUMAN
1 2 3 4
12 0 0 88
$FFAR3_HUMAN
1 2 3 4
12 0 0 88
$GP132_HUMAN
1 2 3 4
12 0 0 88
$GP141_HUMAN
1 2 3 4
12 0 0 88
$GP171_HUMAN
1 2 3 4
12 0 0 88
$GP174_HUMAN
1 2 3 4
12 0 0 88
$GP183_HUMAN
1 2 3 4
1 0 0 99
$GPR17_HUMAN
1 2 3 4
11 0 0 89
$GPR18_HUMAN
1 2 3 4
12 0 0 88
$GPR20_HUMAN
1 2 3 4
12 0 0 88
$GPR31_HUMAN
1 2 3 4
12 0 0 88
$GPR34_HUMAN
1 2 3 4
12 0 0 88
$GPR35_HUMAN
1 2 3 4
12 0 0 88
$GPR4_HUMAN
1 2 3 4
12 0 0 88
$GPR55_HUMAN
1 2 3 4
12 0 0 88
$GPR81_HUMAN
1 2 3 4
12 0 0 88
$GPR82_HUMAN
1 2 3 4
100 0 0 0
$GPR87_HUMAN
1 2 3 4
12 0 0 88
$LPAR4_HUMAN
1 2 3 4
1 0 0 99
$LPAR5_HUMAN
1 2 3 4
12 0 0 88
$NIAR1_HUMAN
1 2 3 4
12 0 0 88
$OGR1_HUMAN
1 2 3 4
12 0 0 88
$OXER1_HUMAN
1 2 3 4
12 0 0 88
$OXGR1_HUMAN
1 2 3 4
0 0 0 100
$P2RY1_HUMAN
1 2 3 4
1 0 0 99
$P2RY2_HUMAN
1 2 3 4
12 0 0 88
$P2RY4_HUMAN
1 2 3 4
12 0 0 88
$P2RY5_HUMAN
1 2 3 4
1 0 0 99
$P2RY6_HUMAN
1 2 3 4
1 0 0 99
$P2RY8_HUMAN
1 2 3 4
12 0 0 88
$P2Y10_HUMAN
1 2 3 4
12 0 0 88
$P2Y11_HUMAN
1 2 3 4
11 0 0 89
$P2Y12_HUMAN
1 2 3 4
12 0 0 88
$P2Y13_HUMAN
1 2 3 4
12 0 0 88
$P2Y14_HUMAN
1 2 3 4
12 0 0 88
$PAR1_HUMAN
1 2 3 4
12 0 0 88
$PAR2_HUMAN
1 2 3 4
12 0 0 88
$PAR3_HUMAN
1 2 3 4
12 0 0 88
$PAR4_HUMAN
1 2 3 4
12 0 0 88
$PSYR_HUMAN
1 2 3 4
12 0 0 88
$PTAFR_HUMAN
1 2 3 4
12 0 0 88
$Q5KU21_HUMAN
1 2 3 4
12 0 0 88
$SUCR1_HUMAN
1 2 3 4
0 0 0 100
$AGTR1_HUMAN
1 2 3 4
0 0 0 100
$AGTR2_HUMAN
1 2 3 4
0 0 0 100
$APJ_HUMAN
1 2 3 4
0 0 0 100
$BKRB1_HUMAN
1 2 3 4
0 0 0 100
$BKRB2_HUMAN
1 2 3 4
0 0 0 100
$C3AR_HUMAN
1 2 3 4
8 0 0 92
$C5ARL_HUMAN
1 2 3 4
11 0 0 89
$C5AR_HUMAN
1 2 3 4
9 0 0 91
$CCBP2_HUMAN
1 2 3 4
0 0 0 100
$CCR10_HUMAN
1 2 3 4
0 0 0 100
$CCR1_HUMAN
1 2 3 4
0 0 0 100
$CCR2_HUMAN
1 2 3 4
0 0 0 100
$CCR3_HUMAN
1 2 3 4
0 0 0 100
$CCR4_HUMAN
1 2 3 4
0 0 0 100
$CCR5_HUMAN
1 2 3 4
0 0 0 100
$CCR6_HUMAN
1 2 3 4
0 0 0 100
$CCR7_HUMAN
1 2 3 4
0 0 0 100
$CCR8_HUMAN
1 2 3 4
0 0 0 100
$CCR9_HUMAN
1 2 3 4
0 0 0 100
$CCRL1_HUMAN
1 2 3 4
0 0 0 100
$CCRL2_HUMAN
1 2 3 4
0 0 0 100
$CML1_HUMAN
1 2 3 4
0 0 0 100
$CX3C1_HUMAN
1 2 3 4
0 0 0 100
$CXCR1_HUMAN
1 2 3 4
0 0 0 100
$CXCR2_HUMAN
1 2 3 4
0 0 0 100
$CXCR3_HUMAN
1 2 3 4
0 0 0 100
$CXCR4_HUMAN
1 2 3 4
0 0 0 100
$CXCR5_HUMAN
1 2 3 4
0 0 0 100
$CXCR6_HUMAN
1 2 3 4
0 0 0 100
$CXCR7_HUMAN
1 2 3 4
0 0 0 100
$FPR1_HUMAN
1 2 3 4
0 0 0 100
$FPR2_HUMAN
1 2 3 4
0 0 0 100
$FPR3_HUMAN
1 2 3 4
0 0 0 100
$GP152_HUMAN
1 2 3 4
99 0 1 0
$GP182_HUMAN
1 2 3 4
0 0 0 100
$GPER_HUMAN
1 2 3 4
0 0 0 100
$GPR15_HUMAN
1 2 3 4
0 0 0 100
$GPR1_HUMAN
1 2 3 4
0 0 0 100
$GPR25_HUMAN
1 2 3 4
0 0 0 100
$GPR32_HUMAN
1 2 3 4
12 0 0 88
$GPR33_HUMAN
1 2 3 4
0 0 0 100
$GPR44_HUMAN
1 2 3 4
12 0 0 88
$LT4R1_HUMAN
1 2 3 4
0 0 100 0
$LT4R2_HUMAN
1 2 3 4
0 0 100 0
$RL3R1_HUMAN
1 2 3 4
0 0 0 100
$RL3R2_HUMAN
1 2 3 4
0 0 0 100
$XCR1_HUMAN
1 2 3 4
0 0 0 100
$MCHR1_HUMAN
1 2 3 4
0 0 100 0
$MCHR2_HUMAN
1 2 3 4
0 0 0 100
$NPBW1_HUMAN
1 2 3 4
0 0 0 100
$NPBW2_HUMAN
1 2 3 4
0 0 0 100
$OPRD_HUMAN
1 2 3 4
0 0 0 100
$OPRK_HUMAN
1 2 3 4
0 0 0 100
$OPRM_HUMAN
1 2 3 4
0 0 0 100
$OPRX_HUMAN
1 2 3 4
0 0 0 100
$SSR1_HUMAN
1 2 3 4
0 0 0 100
$SSR2_HUMAN
1 2 3 4
0 0 0 100
$SSR3_HUMAN
1 2 3 4
0 0 0 100
$SSR4_HUMAN
1 2 3 4
0 0 0 100
$SSR5_HUMAN
1 2 3 4
0 0 0 100
$UR2R_HUMAN
1 2 3 4
0 0 100 0
$BRS3_HUMAN
1 2 3 4
0 0 100 0
$CCKAR_HUMAN
1 2 3 4
0 0 100 0
$EDNRA_HUMAN
1 2 3 4
0 0 100 0
$EDNRB_HUMAN
1 2 3 4
0 0 100 0
$ETBR2_HUMAN
1 2 3 4
0 0 100 0
$GALR1_HUMAN
1 2 3 4
0 0 100 0
$GALR2_HUMAN
1 2 3 4
0 0 100 0
$GALR3_HUMAN
1 2 3 4
0 0 100 0
$GASR_HUMAN
1 2 3 4
0 0 100 0
$GHSR_HUMAN
1 2 3 4
0 0 100 0
$GNRHR_HUMAN
1 2 3 4
0 0 100 0
$GNRR2_HUMAN
1 2 3 4
0 0 100 0
$GP101_HUMAN
1 2 3 4
0 0 100 0
$GP135_HUMAN
1 2 3 4
0 0 100 0
$GP151_HUMAN
1 2 3 4
0 0 100 0
$GP173_HUMAN
1 2 3 4
0 0 100 0
$GP176_HUMAN
1 2 3 4
0 0 100 0
$GPR19_HUMAN
1 2 3 4
0 0 100 0
$GPR27_HUMAN
1 2 3 4
0 0 100 0
$GPR37_HUMAN
1 2 3 4
0 0 100 0
$GPR39_HUMAN
1 2 3 4
0 0 100 0
$GPR83_HUMAN
1 2 3 4
0 0 100 0
$GPR84_HUMAN
1 2 3 4
0 0 100 0
$GPR85_HUMAN
1 2 3 4
0 0 100 0
$GRPR_HUMAN
1 2 3 4
0 0 100 0
$KISSR_HUMAN
1 2 3 4
0 0 100 0
$MTLR_HUMAN
1 2 3 4
0 0 100 0
$NK1R_HUMAN
1 2 3 4
0 0 100 0
$NK2R_HUMAN
1 2 3 4
0 0 100 0
$NK3R_HUMAN
1 2 3 4
0 0 100 0
$NMBR_HUMAN
1 2 3 4
0 0 100 0
$NMUR1_HUMAN
1 2 3 4
0 0 100 0
$NMUR2_HUMAN
1 2 3 4
0 0 100 0
$NPFF1_HUMAN
1 2 3 4
0 0 100 0
$NPFF2_HUMAN
1 2 3 4
0 0 100 0
$NPSR1_HUMAN
1 2 3 4
0 0 100 0
$NPY1R_HUMAN
1 2 3 4
0 0 100 0
$NPY2R_HUMAN
1 2 3 4
0 0 100 0
$NPY4R_HUMAN
1 2 3 4
0 0 100 0
$NPY5R_HUMAN
1 2 3 4
0 0 100 0
$NTR1_HUMAN
1 2 3 4
0 0 100 0
$NTR2_HUMAN
1 2 3 4
0 0 100 0
$OX1R_HUMAN
1 2 3 4
0 0 100 0
$OX2R_HUMAN
1 2 3 4
0 0 100 0
$OXYR_HUMAN
1 2 3 4
0 0 100 0
$PKR1_HUMAN
1 2 3 4
0 0 100 0
$PKR2_HUMAN
1 2 3 4
0 0 100 0
$PRLHR_HUMAN
1 2 3 4
0 0 100 0
$QRFPR_HUMAN
1 2 3 4
0 0 100 0
$TRFR_HUMAN
1 2 3 4
0 0 100 0
$V1AR_HUMAN
1 2 3 4
0 0 100 0
$V1BR_HUMAN
1 2 3 4
0 0 100 0
$V2R_HUMAN
1 2 3 4
0 0 100 0
$MTR1A_HUMAN
1 2 3 4
0 0 100 0
$MTR1B_HUMAN
1 2 3 4
0 0 100 0
$MTR1L_HUMAN
1 2 3 4
0 0 100 0
$OPN3_HUMAN
1 2 3 4
0 0 100 0
$OPN4_HUMAN
1 2 3 4
0 0 100 0
$OPN5_HUMAN
1 2 3 4
0 0 100 0
$OPSB_HUMAN
1 2 3 4
0 0 100 0
$OPSD_HUMAN
1 2 3 4
0 0 100 0
$OPSR_HUMAN
1 2 3 4
0 0 100 0
$OPSX_HUMAN
1 2 3 4
0 0 100 0
$RGR_HUMAN
1 2 3 4
88 0 12 0
$FSHR_HUMAN
1 2 3 4
88 0 12 0
$LSHR_HUMAN
1 2 3 4
88 0 12 0
$TSHR_HUMAN
1 2 3 4
88 0 12 0
$LGR4_HUMAN
1 2 3 4
88 0 12 0
$LGR5_HUMAN
1 2 3 4
88 0 12 0
$LGR6_HUMAN
1 2 3 4
88 0 12 0
$RXFP1_HUMAN
1 2 3 4
52 0 48 0
$RXFP2_HUMAN
1 2 3 4
0 0 100 0
$PD2R_HUMAN
1 2 3 4
88 0 12 0
$PE2R1_HUMAN
1 2 3 4
88 0 12 0
$PE2R2_HUMAN
1 2 3 4
88 0 12 0
$PE2R3_HUMAN
1 2 3 4
88 0 12 0
$PE2R4_HUMAN
1 2 3 4
88 0 12 0
$PF2R_HUMAN
1 2 3 4
88 0 12 0
$PI2R_HUMAN
1 2 3 4
88 0 12 0
$TA2R_HUMAN
1 2 3 4
88 0 12 0
$MAS_HUMAN
1 2 3 4
99 0 1 0
$MRGRD_HUMAN
1 2 3 4
99 0 1 0
$MRGRF_HUMAN
1 2 3 4
99 0 1 0
$MAS1L_HUMAN
1 2 3 4
99 0 1 0
$MRGRE_HUMAN
1 2 3 4
99 0 1 0
$MRGRG_HUMAN
1 2 3 4
99 0 1 0
$MRGX1_HUMAN
1 2 3 4
99 0 1 0
$MRGX2_HUMAN
1 2 3 4
99 0 1 0
$MRGX3_HUMAN
1 2 3 4
99 0 1 0
$MRGX4_HUMAN
1 2 3 4
99 0 1 0
$ACTHR_HUMAN
1 2 3 4
71 29 0 0
$MC3R_HUMAN
1 2 3 4
0 100 0 0
$MC4R_HUMAN
1 2 3 4
0 100 0 0
$MC5R_HUMAN
1 2 3 4
52 48 0 0
$MSHR_HUMAN
1 2 3 4
88 12 0 0
$GP119_HUMAN
1 2 3 4
52 48 0 0
$GPR12_HUMAN
1 2 3 4
88 12 0 0
$GPR3_HUMAN
1 2 3 4
88 12 0 0
$GPR6_HUMAN
1 2 3 4
88 12 0 0
$S1PR1_HUMAN
1 2 3 4
88 12 0 0
$S1PR2_HUMAN
1 2 3 4
88 12 0 0
$S1PR3_HUMAN
1 2 3 4
88 12 0 0
$S1PR4_HUMAN
1 2 3 4
88 0 12 0
$S1PR5_HUMAN
1 2 3 4
88 0 12 0
$CNR1_HUMAN
1 2 3 4
88 12 0 0
$CNR2_HUMAN
1 2 3 4
88 12 0 0
$LPAR1_HUMAN
1 2 3 4
88 12 0 0
$LPAR2_HUMAN
1 2 3 4
88 11 1 0
$LPAR3_HUMAN
1 2 3 4
88 12 0 0
$AA1R_HUMAN
1 2 3 4
0 100 0 0
$AA2AR_HUMAN
1 2 3 4
0 100 0 0
$AA2BR_HUMAN
1 2 3 4
0 100 0 0
$AA3R_HUMAN
1 2 3 4
0 100 0 0
$`5HT1A_HUMAN`
1 2 3 4
0 100 0 0
$`5HT1B_HUMAN`
1 2 3 4
0 100 0 0
$`5HT1D_HUMAN`
1 2 3 4
0 100 0 0
$`5HT1E_HUMAN`
1 2 3 4
0 100 0 0
$`5HT1F_HUMAN`
1 2 3 4
0 100 0 0
$`5HT2A_HUMAN`
1 2 3 4
0 100 0 0
$`5HT2B_HUMAN`
1 2 3 4
0 100 0 0
$`5HT2C_HUMAN`
1 2 3 4
0 100 0 0
$`5HT4R_HUMAN`
1 2 3 4
0 100 0 0
$`5HT5A_HUMAN`
1 2 3 4
0 100 0 0
$`5HT6R_HUMAN`
1 2 3 4
0 100 0 0
$`5HT7R_HUMAN`
1 2 3 4
0 100 0 0
$ACM1_HUMAN
1 2 3 4
0 100 0 0
$ACM2_HUMAN
1 2 3 4
0 100 0 0
$ACM3_HUMAN
1 2 3 4
0 100 0 0
$ACM4_HUMAN
1 2 3 4
0 100 0 0
$ACM5_HUMAN
1 2 3 4
0 100 0 0
$ADA1A_HUMAN
1 2 3 4
0 100 0 0
$ADA1B_HUMAN
1 2 3 4
0 100 0 0
$ADA1D_HUMAN
1 2 3 4
0 100 0 0
$ADA2A_HUMAN
1 2 3 4
0 100 0 0
$ADA2B_HUMAN
1 2 3 4
0 100 0 0
$ADA2C_HUMAN
1 2 3 4
0 100 0 0
$ADRB1_HUMAN
1 2 3 4
0 100 0 0
$ADRB2_HUMAN
1 2 3 4
0 100 0 0
$ADRB3_HUMAN
1 2 3 4
0 100 0 0
$DRD1_HUMAN
1 2 3 4
0 100 0 0
$DRD2_HUMAN
1 2 3 4
0 100 0 0
$DRD3_HUMAN
1 2 3 4
0 100 0 0
$DRD4_HUMAN
1 2 3 4
0 100 0 0
$DRD5_HUMAN
1 2 3 4
0 100 0 0
$HRH1_HUMAN
1 2 3 4
0 100 0 0
$HRH2_HUMAN
1 2 3 4
0 100 0 0
$HRH3_HUMAN
1 2 3 4
0 100 0 0
$HRH4_HUMAN
1 2 3 4
0 100 0 0
$TAAR1_HUMAN
1 2 3 4
0 100 0 0
$TAAR2_HUMAN
1 2 3 4
0 100 0 0
$TAAR3_HUMAN
1 2 3 4
0 100 0 0
$TAAR5_HUMAN
1 2 3 4
0 100 0 0
$TAAR6_HUMAN
1 2 3 4
0 100 0 0
$TAAR8_HUMAN
1 2 3 4
0 100 0 0
$TAAR9_HUMAN
1 2 3 4
0 100 0 0
$GP120_HUMAN
1 2 3 4
0 0 100 0
$GP139_HUMAN
1 2 3 4
0 0 100 0
$GP142_HUMAN
1 2 3 4
0 0 100 0
$GP146_HUMAN
1 2 3 4
0 0 100 0
$GP148_HUMAN
1 2 3 4
88 0 12 0
$GP150_HUMAN
1 2 3 4
88 0 12 0
$GP160_HUMAN
1 2 3 4
88 0 12 0
$GP161_HUMAN
1 2 3 4
0 0 100 0
$GPBAR_HUMAN
1 2 3 4
88 0 12 0
$GPR21_HUMAN
1 2 3 4
0 0 100 0
$GPR22_HUMAN
1 2 3 4
0 0 100 0
$GPR26_HUMAN
1 2 3 4
88 0 12 0
$GPR45_HUMAN
1 2 3 4
0 0 100 0
$GPR52_HUMAN
1 2 3 4
0 0 100 0
$GPR61_HUMAN
1 2 3 4
0 0 100 0
$GPR62_HUMAN
1 2 3 4
60 0 40 0
$GPR63_HUMAN
1 2 3 4
0 0 100 0
$GPR75_HUMAN
1 2 3 4
88 0 12 0
$GPR78_HUMAN
1 2 3 4
88 0 12 0
$GPR88_HUMAN
1 2 3 4
52 0 48 0
$Q5KU14_HUMAN
1 2 3 4
0 0 100 0
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