HDMD-package: Structural Analysis Tools for High Dimensional Molecular Data

Description Details Author(s) References See Also Examples

Description

High Dimensional Molecular Data (HDMD) typically have many more variables or dimensions than observations or replicates (D>>N). This can cause many statistical procedures to fail, become intractable, or produce misleading results. This package provides several tools covering Factor Analysis (FA), Principal Components Analysis (PCA) and Discriminant Analysis (DA) to reduce dimensionality and analyze biological data for meaningful interpretation of results. Since genetic (DNA or Amino Acid) sequences are composed of discrete alphabetic characters, entropy and mutual information are often used to estimate variability and covariability, respectively. Alternatively, discrete alphabetic sequences can be transformed into biologically informative metrics to be used in various multivariate procedures. This package provide moleculr entropy and mutual information estimates as well as a metric transformation to convert amino acid letters into indices determined by Atchley et al 2005.

Details

Package: HDMD
Type: Package
Version: 1.1
Date: 2012-9-19
License: GPL (>=2)
LazyLoad: yes

Author(s)

Lisa McFerrin Maintainer: Lisa McFerrin <lgmcferr@ncsu.edu>

References

Atchley, W.R., Zhao, J., Fernandes, A. and Drueke, T. (2005) Solving the sequence "metric" problem: Proc. Natl. Acad. Sci. USA 102: 6395-6400

Atchley, W.R. and Fernandes, A. (2005) Sequence signatures an the probabilisitic identification of proteins in the Myc-Max-Mad network. Proc. Natl. Acad. Sci. USa 102: 6401-6406

Revelle, W. (in preparation) An Introduction to Psychometric Theory with applications in R. Springer at http://personality-project.org/r/book

See Also

psych ~~

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
data(AA54)
#perform Factor Analysis on HDMD where D>>N
Factor54 = factor.pa.ginv(AA54, nfactors = 5, m=3, prerotate=TRUE, rotate="Promax", scores="regression")
Factor54

data(bHLH288)
bHLH_Seq = as.vector(bHLH288[,2])
grouping = t(bHLH288[,1])

#Transform Amino Acid Data into a biologically meaninful metric
AA54_MetricFactor1 = FactorTransform(bHLH_Seq, Replace=AAMetric, Factor=1, alignment=TRUE)

#Calculate the pairwise mahalanobis distances among groups given a discriminant function 
AA54_lda_Metric1 = lda(AA54_MetricFactor1, grouping)
AA54_lda_RawMetric1 = as.matrix(AA54_MetricFactor1) 
AA54_lda_RawMetric1Centered = scale(AA54_lda_RawMetric1, center = TRUE, scale = FALSE)
AA54_lda_RawMetric1Centered[c(20:25, 137:147, 190:196, 220:229, 264:273),1:8]
plot(-1*AA54_lda_RawMetric1Centered[,1], -1*AA54_lda_RawMetric1Centered[,2], pch = grouping, xlab="Canonical Variate 1", ylab="Canonical Variate 2", main="DA Scores (Centered Raw Coefficients)\nusing Factor1 (pah) from R transformation")
lines(c(0,0), c(-15,15), lty="dashed")
lines(c(-35,25), c(0,0), lty="dashed")

Mahala_1 = pairwise.mahalanobis(AA54_lda_RawMetric1Centered, grouping)
D = sqrt(Mahala_1$distance)
D

Example output

Loading required package: psych
Loading required package: MASS
Warning message:
In data(AA54) : data set 'AA54' not found
Could not solve for inverse correlation.  Using general inverse ginv(r) 
Warning message:
In cor.smooth(R) : Matrix was not positive definite, smoothing was done
Factor Analysis using method = 
Call: NULL

 Warning: A Heywood case was detected. 
Unstandardized loadings (pattern matrix) based upon covariance matrix
                                                     F1    F2    F3    F4    F5
Conformational parameter of beta-turn              0.24  0.68 -0.17 -0.43 -0.07
Chou-Fasman parameter of the coil conformation     0.20  0.77 -0.34 -0.05 -0.05
Average volume of buried residue                   0.30 -0.13  0.81 -0.34 -0.02
Residue accessible surface area in folded protein  0.97  0.11  0.21  0.03 -0.24
Normalized frequency of beta-sheet                -0.48  0.04  0.58  0.02 -0.11
Normalized frequency of beta-turn                  0.41  0.63 -0.35 -0.02  0.08
Normalized frequency of turn                       0.08  0.82 -0.08 -0.39  0.05
Size                                               0.48 -0.08  0.85 -0.15 -0.11
Amino acid composition                             0.10 -0.01 -0.28  0.85 -0.06
Relative mutability                                0.33 -0.17 -0.20  0.30  0.29
Molecular weight                                   0.39 -0.08  0.70 -0.50  0.05
Number of hydrogen bond donors                     0.83  0.03  0.15  0.01 -0.36
Positive charge                                    0.44 -0.25 -0.20 -0.10 -0.70
Negative charge                                    0.44 -0.23 -0.02 -0.04  0.70
Helix-coil equilibrium constant                    0.11 -0.71  0.39 -0.12 -0.05
Alpha-helix indices                                0.12 -0.95 -0.17 -0.22 -0.01
Hydrophobicity factor                             -0.19  0.23  0.84 -0.01  0.10
Residue volume                                     0.26 -0.15  0.83 -0.30 -0.04
Polarity                                           0.78 -0.06 -0.38  0.03  0.08
Hydrophobicity value                               0.77 -0.16 -0.33  0.21 -0.03
Heat capacity                                     -0.17 -0.38  0.18 -0.65  0.00
Normalized relative frequency of bend              0.44  0.66 -0.23  0.08  0.11
Normalized relative frequency of coil             -0.07  0.33 -0.59 -0.08 -0.13
Average accessible surface area                    1.02 -0.02  0.19  0.05 -0.16
Percentage of buried residues                     -1.03 -0.13 -0.19 -0.07 -0.03
Percentage of exposed residues                     1.04  0.03  0.22  0.09 -0.03
Transfer free energy                              -1.02 -0.04 -0.14 -0.11  0.15
Relative frequency of occurrence                   0.12 -0.10 -0.12  0.92 -0.01
Average relative probability of helix              0.13 -1.01 -0.16 -0.07  0.04
Net charge                                         0.09  0.06  0.01  0.13 -0.96
Side chain volume                                  0.21 -0.18  0.79 -0.30 -0.09
Hydropathy index                                  -0.86 -0.16  0.10  0.22  0.03
Normalized frequency of beta-sheet unweighted     -0.43  0.13  0.61  0.12 -0.04
Normalized frequency of left-handed alpha-helix   -0.10  0.34 -0.65 -0.07 -0.27
Refractivity                                      -0.04 -0.06  0.51 -0.62 -0.09
Average side chain orientation angle              -0.90 -0.16 -0.01 -0.11 -0.18
Normalized frequency coil                          0.29  0.87  0.03  0.12 -0.08
AA composition of total proteins                   0.16 -0.14 -0.08  0.95 -0.05
Average non-bonded energy per atom                 1.04  0.08  0.18  0.04  0.07
Long range non-bonded energy per atom              0.71 -0.03 -0.39  0.19  0.09
Average non-bonded energy per residue              0.04  0.36  0.02 -0.50  0.30
Optimized propensity to form reverse turn          0.21 -0.02 -0.45  0.32  0.19
Relative frequency in alpha-helix                  0.04 -1.00 -0.26 -0.22 -0.02
Information measure for pleated-sheet             -0.51 -0.11  0.44  0.06 -0.17
Information measure for loop                       0.20  0.77 -0.18 -0.33 -0.18
Normalized frequency of extended structure        -0.36  0.36  0.70  0.15 -0.05
Average interactions per side chain atom          -0.94 -0.13 -0.17  0.06 -0.13
Polar requirement                                  0.76 -0.14 -0.33 -0.02  0.24
Bulkiness                                          0.00 -0.07  1.00  0.06  0.24
Isolelectric point                                 0.24 -0.04 -0.03  0.14 -0.96
Free energy in alpha-helical region               -0.17  0.85 -0.01 -0.09  0.10
Free energy in beta-strand region                  0.19  0.44 -0.13  0.13  0.15
Number of codon(s)                                 0.10  0.16  0.06  0.85 -0.30
Solvation free energy                             -0.87  0.01  0.15  0.01  0.27
                                                    h2   u2   H2    U2
Conformational parameter of beta-turn             0.84 0.16 0.84 0.160
Chou-Fasman parameter of the coil conformation    0.96 0.05 0.95 0.050
Average volume of buried residue                  0.93 0.07 0.93 0.070
Residue accessible surface area in folded protein 0.96 0.04 0.96 0.040
Normalized frequency of beta-sheet                0.79 0.20 0.80 0.201
Normalized frequency of beta-turn                 0.97 0.03 0.97 0.030
Normalized frequency of turn                      0.87 0.14 0.86 0.138
Size                                              0.92 0.08 0.92 0.080
Amino acid composition                            0.88 0.13 0.87 0.129
Relative mutability                               0.42 0.58 0.42 0.579
Molecular weight                                  0.91 0.08 0.92 0.080
Number of hydrogen bond donors                    0.82 0.19 0.81 0.189
Positive charge                                   0.73 0.27 0.73 0.270
Negative charge                                   0.73 0.26 0.74 0.263
Helix-coil equilibrium constant                   0.86 0.15 0.85 0.149
Alpha-helix indices                               0.90 0.11 0.89 0.109
Hydrophobicity factor                             0.72 0.27 0.73 0.272
Residue volume                                    0.95 0.05 0.95 0.050
Polarity                                          0.96 0.04 0.96 0.040
Hydrophobicity value                              0.86 0.14 0.86 0.140
Heat capacity                                     0.72 0.28 0.72 0.280
Normalized relative frequency of bend             0.91 0.09 0.91 0.090
Normalized relative frequency of coil             0.49 0.51 0.49 0.510
Average accessible surface area                   0.99 0.01 0.99 0.010
Percentage of buried residues                     0.96 0.03 0.97 0.030
Percentage of exposed residues                    0.96 0.03 0.97 0.030
Transfer free energy                              0.99 0.02 0.98 0.020
Relative frequency of occurrence                  0.89 0.10 0.90 0.101
Average relative probability of helix             0.98 0.02 0.98 0.020
Net charge                                        0.93 0.07 0.93 0.070
Side chain volume                                 0.95 0.05 0.95 0.050
Hydropathy index                                  0.95 0.05 0.95 0.050
Normalized frequency of beta-sheet unweighted     0.71 0.29 0.71 0.289
Normalized frequency of left-handed alpha-helix   0.55 0.44 0.56 0.443
Refractivity                                      0.86 0.15 0.85 0.149
Average side chain orientation angle              0.86 0.14 0.86 0.140
Normalized frequency coil                         0.87 0.14 0.86 0.139
AA composition of total proteins                  0.92 0.07 0.93 0.070
Average non-bonded energy per atom                0.98 0.02 0.98 0.020
Long range non-bonded energy per atom             0.89 0.09 0.91 0.092
Average non-bonded energy per residue             0.43 0.57 0.43 0.569
Optimized propensity to form reverse turn         0.56 0.44 0.56 0.441
Relative frequency in alpha-helix                 0.95 0.05 0.95 0.050
Information measure for pleated-sheet             0.73 0.28 0.72 0.276
Information measure for loop                      0.91 0.09 0.91 0.090
Normalized frequency of extended structure        0.78 0.22 0.78 0.221
Average interactions per side chain atom          0.84 0.16 0.84 0.160
Polar requirement                                 0.95 0.06 0.94 0.060
Bulkiness                                         0.89 0.10 0.90 0.101
Isolelectric point                                0.96 0.05 0.95 0.050
Free energy in alpha-helical region               0.75 0.25 0.75 0.251
Free energy in beta-strand region                 0.37 0.63 0.37 0.633
Number of codon(s)                                0.77 0.22 0.78 0.222
Solvation free energy                             0.92 0.09 0.91 0.089

                         F1   F2   F3   F4   F5
SS loadings           15.37 9.74 9.97 6.14 3.92
Proportion Var         0.28 0.18 0.18 0.11 0.07
Cumulative Var         0.28 0.47 0.65 0.76 0.84
Proportion Explained   0.34 0.22 0.22 0.14 0.09
Cumulative Proportion  0.34 0.56 0.78 0.91 1.00

 Standardized loadings (pattern matrix)
                                                  item    F1    F2    F3    F4
Conformational parameter of beta-turn                1  0.24  0.68 -0.17 -0.43
Chou-Fasman parameter of the coil conformation       2  0.20  0.77 -0.34 -0.05
Average volume of buried residue                     3  0.30 -0.13  0.81 -0.34
Residue accessible surface area in folded protein    4  0.97  0.11  0.21  0.03
Normalized frequency of beta-sheet                   5 -0.48  0.04  0.58  0.02
Normalized frequency of beta-turn                    6  0.41  0.63 -0.35 -0.02
Normalized frequency of turn                         7  0.08  0.81 -0.08 -0.39
Size                                                 8  0.48 -0.08  0.85 -0.15
Amino acid composition                               9  0.10 -0.01 -0.28  0.85
Relative mutability                                 10  0.33 -0.17 -0.20  0.30
Molecular weight                                    11  0.39 -0.08  0.70 -0.50
Number of hydrogen bond donors                      12  0.83  0.03  0.15  0.01
Positive charge                                     13  0.44 -0.25 -0.20 -0.10
Negative charge                                     14  0.44 -0.23 -0.02 -0.04
Helix-coil equilibrium constant                     15  0.11 -0.71  0.39 -0.12
Alpha-helix indices                                 16  0.12 -0.95 -0.17 -0.22
Hydrophobicity factor                               17 -0.19  0.23  0.84 -0.01
Residue volume                                      18  0.26 -0.15  0.83 -0.30
Polarity                                            19  0.78 -0.06 -0.38  0.03
Hydrophobicity value                                20  0.77 -0.16 -0.33  0.21
Heat capacity                                       21 -0.17 -0.38  0.18 -0.65
Normalized relative frequency of bend               22  0.44  0.66 -0.23  0.08
Normalized relative frequency of coil               23 -0.07  0.33 -0.59 -0.08
Average accessible surface area                     24  1.02 -0.02  0.19  0.05
Percentage of buried residues                       25 -1.03 -0.13 -0.19 -0.07
Percentage of exposed residues                      26  1.04  0.03  0.22  0.09
Transfer free energy                                27 -1.02 -0.04 -0.14 -0.11
Relative frequency of occurrence                    28  0.12 -0.10 -0.12  0.92
Average relative probability of helix               29  0.13 -1.01 -0.16 -0.07
Net charge                                          30  0.09  0.06  0.01  0.13
Side chain volume                                   31  0.21 -0.18  0.79 -0.30
Hydropathy index                                    32 -0.86 -0.16  0.10  0.22
Normalized frequency of beta-sheet unweighted       33 -0.43  0.13  0.61  0.12
Normalized frequency of left-handed alpha-helix     34 -0.10  0.34 -0.65 -0.07
Refractivity                                        35 -0.04 -0.06  0.51 -0.62
Average side chain orientation angle                36 -0.90 -0.16 -0.01 -0.11
Normalized frequency coil                           37  0.29  0.87  0.03  0.12
AA composition of total proteins                    38  0.16 -0.14 -0.08  0.95
Average non-bonded energy per atom                  39  1.04  0.08  0.18  0.04
Long range non-bonded energy per atom               40  0.72 -0.03 -0.39  0.19
Average non-bonded energy per residue               41  0.04  0.36  0.02 -0.50
Optimized propensity to form reverse turn           42  0.21 -0.02 -0.45  0.32
Relative frequency in alpha-helix                   43  0.04 -1.00 -0.26 -0.22
Information measure for pleated-sheet               44 -0.51 -0.11  0.44  0.06
Information measure for loop                        45  0.20  0.77 -0.18 -0.33
Normalized frequency of extended structure          46 -0.36  0.36  0.70  0.15
Average interactions per side chain atom            47 -0.94 -0.13 -0.17  0.06
Polar requirement                                   48  0.76 -0.14 -0.33 -0.02
Bulkiness                                           49  0.00 -0.07  1.00  0.06
Isolelectric point                                  50  0.24 -0.04 -0.03  0.14
Free energy in alpha-helical region                 51 -0.17  0.85 -0.01 -0.09
Free energy in beta-strand region                   52  0.19  0.44 -0.13  0.13
Number of codon(s)                                  53  0.10  0.16  0.06  0.85
Solvation free energy                               54 -0.87  0.01  0.15  0.01
                                                     F5   h2    u2
Conformational parameter of beta-turn             -0.07 0.84 0.160
Chou-Fasman parameter of the coil conformation    -0.05 0.95 0.050
Average volume of buried residue                  -0.02 0.93 0.070
Residue accessible surface area in folded protein -0.24 0.96 0.040
Normalized frequency of beta-sheet                -0.11 0.80 0.201
Normalized frequency of beta-turn                  0.08 0.97 0.030
Normalized frequency of turn                       0.05 0.86 0.138
Size                                              -0.11 0.92 0.080
Amino acid composition                            -0.06 0.87 0.129
Relative mutability                                0.29 0.42 0.579
Molecular weight                                   0.05 0.92 0.080
Number of hydrogen bond donors                    -0.36 0.81 0.189
Positive charge                                   -0.70 0.73 0.270
Negative charge                                    0.70 0.74 0.263
Helix-coil equilibrium constant                   -0.05 0.85 0.149
Alpha-helix indices                               -0.01 0.89 0.109
Hydrophobicity factor                              0.10 0.73 0.272
Residue volume                                    -0.04 0.95 0.050
Polarity                                           0.08 0.96 0.040
Hydrophobicity value                              -0.03 0.86 0.140
Heat capacity                                      0.00 0.72 0.280
Normalized relative frequency of bend              0.11 0.91 0.090
Normalized relative frequency of coil             -0.13 0.49 0.510
Average accessible surface area                   -0.16 0.99 0.010
Percentage of buried residues                     -0.03 0.97 0.030
Percentage of exposed residues                    -0.03 0.97 0.030
Transfer free energy                               0.15 0.98 0.020
Relative frequency of occurrence                  -0.01 0.90 0.101
Average relative probability of helix              0.04 0.98 0.020
Net charge                                        -0.96 0.93 0.070
Side chain volume                                 -0.09 0.95 0.050
Hydropathy index                                   0.03 0.95 0.050
Normalized frequency of beta-sheet unweighted     -0.04 0.71 0.289
Normalized frequency of left-handed alpha-helix   -0.27 0.56 0.443
Refractivity                                      -0.09 0.85 0.149
Average side chain orientation angle              -0.18 0.86 0.140
Normalized frequency coil                         -0.08 0.86 0.139
AA composition of total proteins                  -0.05 0.93 0.070
Average non-bonded energy per atom                 0.07 0.98 0.020
Long range non-bonded energy per atom              0.09 0.91 0.092
Average non-bonded energy per residue              0.30 0.43 0.569
Optimized propensity to form reverse turn          0.19 0.56 0.441
Relative frequency in alpha-helix                 -0.02 0.95 0.050
Information measure for pleated-sheet             -0.17 0.72 0.276
Information measure for loop                      -0.18 0.91 0.090
Normalized frequency of extended structure        -0.05 0.78 0.221
Average interactions per side chain atom          -0.13 0.84 0.160
Polar requirement                                  0.24 0.94 0.060
Bulkiness                                          0.24 0.90 0.101
Isolelectric point                                -0.96 0.95 0.050
Free energy in alpha-helical region                0.10 0.75 0.251
Free energy in beta-strand region                  0.15 0.37 0.633
Number of codon(s)                                -0.30 0.78 0.222
Solvation free energy                              0.27 0.91 0.089

                   F1   F2   F3   F4   F5
SS loadings     15.38 9.74 9.97 6.14 3.92
Proportion Var   0.28 0.18 0.18 0.11 0.07
Cumulative Var   0.28 0.47 0.65 0.76 0.84
Cum. factor Var  0.34 0.56 0.78 0.91 1.00

 With factor correlations of 
      F1    F2    F3    F4    F5
F1  1.00  0.06 -0.33 -0.14 -0.02
F2  0.06  1.00 -0.30  0.02 -0.01
F3 -0.33 -0.30  1.00 -0.20 -0.40
F4 -0.14  0.02 -0.20  1.00  0.10
F5 -0.02 -0.01 -0.40  0.10  1.00

Test of the hypothesis that 5 factors are sufficient.

The degrees of freedom for the model are 1171  and the objective function was  Inf 
The total number of observations was  20  with Likelihood Chi Square =  0  with prob <  1 

Fit based upon off diagonal values = 0.99Warning message:
In data(bHLH288) : data set 'bHLH288' not found
              [,1]        [,2]       [,3]        [,4]       [,5]       [,6]
Seq20   0.30472048  0.21026915  1.6380340 -0.66701460 -0.7759400 -0.7519688
Seq21   0.30472048  0.21026915  1.6380340 -0.66701460 -0.7759400 -0.7519688
Seq22   0.30472048  0.21026915  1.3430338 -0.66701460 -0.7759400 -0.7519688
Seq23   0.30472048  0.21026915 -1.1629914 -0.66701460 -0.7759400  0.1499192
Seq24   0.30472048  0.21026915 -1.1629914 -0.66701460 -0.7759400  0.1499192
Seq25   0.30472048  0.21026915 -1.1629914 -0.66701460 -0.7759400  0.1499192
Seq137  0.30472048  0.21026915  1.3430338  0.83121906  0.1579891  0.1499192
Seq138  0.30472048  0.21026915  1.3430338  0.83121906  0.1579891  0.1499192
Seq139  0.59972074  0.21026915 -0.7912217 -1.31461183  0.1579891  0.1499192
Seq140  0.30472048  0.21026915 -0.7912217  0.83121906  0.1579891  0.1499192
Seq141  0.59972074  0.21026915  0.7070120  0.84036986  0.1579891  0.1499192
Seq142  0.30472048  0.50526941 -0.7950249  1.76224108  0.1579891 -2.0672840
Seq143 -0.33130128  0.21026915 -0.1496912 -0.02548416  0.1579891  0.1499192
Seq144 -0.33130128  0.21026915 -0.1496912 -0.02548416  0.1579891  0.1499192
Seq145 -1.16259952  0.21026915 -0.1496912 -0.07066890  0.1579891  0.1499192
Seq146 -0.33130128  0.21026915 -0.1496912 -0.07066890  0.1579891  0.1499192
Seq147 -1.18800450  0.21026915 -0.1496912 -0.07066890  0.1579891  0.1499192
Seq190 -0.02153163 -1.84505560 -1.5101912 -0.07066890  1.6533157 -0.7067840
Seq191 -0.02153163 -1.84505560 -1.5101912 -1.33657797  1.6533157 -0.7067840
Seq192  0.30472048  0.50526941  1.1107425  1.76224108 -0.1344096  0.7859409
Seq193  0.30472048  0.50526941  1.1107425  1.76224108 -0.1344096  0.7859409
Seq194  0.30472048  0.50526941  1.1107425  1.76224108 -0.1344096  0.7859409
Seq195  0.30472048  0.50526941  1.1107425  1.76224108 -0.1344096  0.7859409
Seq196  0.30472048  0.50526941  1.1107425  1.76224108 -0.1344096  0.7859409
Seq220 -1.82953494 -0.02202209 -0.7912217 -0.66701460 -0.7759400  0.4596888
Seq221 -2.47713217  0.50526941 -0.7122910 -0.58808393  1.1260242  0.5536497
Seq222  0.59972074 -1.84505560 -0.7122910  0.15786845 -1.1477098  0.5536497
Seq223 -0.89560587  0.50526941 -0.7122910  0.15786845 -0.6970093 -2.0672840
Seq224  0.59972074 -1.84505560  0.7070120  0.15786845 -0.7759400 -1.3483145
Seq225 -1.00465189 -1.09910322 -0.1496912  0.15786845 -1.4455034 -1.7200843
Seq226 -2.47713217  0.50526941 -0.9129898  1.23494958  1.0320633  0.5536497
Seq227 -0.33130128  0.50526941 -0.1496912  0.15786845 -0.7759400 -1.7200843
Seq228  0.59972074 -2.59354964  0.0336614 -1.03878439 -1.1477098  0.4596888
Seq229  0.59972074 -2.59354964  0.0336614 -1.03878439 -1.1477098  0.4596888
Seq264  0.30472048  0.50526941  0.7070120 -1.03878439  1.6533157 -0.5234314
Seq265  0.30472048  0.50526941 -0.1496912 -1.03878439  1.6533157 -0.5234314
Seq266  0.30472048  0.50526941 -0.1496912 -1.03878439  1.6533157 -0.5234314
Seq267 -0.32215048  0.50526941  1.6380340  0.83121906  1.6533157 -0.5234314
Seq268  0.30472048  0.50526941 -0.1948760  0.83121906  1.6533157 -0.5234314
Seq269 -1.16259952  0.50526941 -1.1629914  0.15786845  0.1579891  0.7859409
Seq270 -1.16259952  0.50526941 -1.1629914  0.15786845  0.1579891  0.7859409
Seq271 -1.16259952  0.50526941 -1.1629914  0.15786845  0.1579891  0.7859409
Seq272  0.59972074  0.50526941 -1.5101912 -0.02548416  1.6533157 -0.5234314
Seq273 -2.47713217 -1.92778953 -1.4607850 -0.02548416  1.6533157 -0.5234314
             [,7]        [,8]
Seq20  -0.7654239  1.27967739
Seq21  -0.7654239  1.27967739
Seq22  -1.0154256  1.27967739
Seq23  -0.6436558  1.27967739
Seq24  -0.6436558  1.27967739
Seq25  -0.6436558  1.27967739
Seq137 -1.3132192 -1.22634782
Seq138  1.4905996 -0.97634616
Seq139 -1.3626253 -1.22634782
Seq140 -1.3626253 -1.22634782
Seq141  1.1643475 -0.97634616
Seq142  0.8637287 -0.97634616
Seq143  1.2583084 -1.22634782
Seq144  1.2583084 -1.22634782
Seq145  1.2583084 -1.22634782
Seq146  1.2583084 -1.22634782
Seq147  1.2583084 -0.97634616
Seq190  0.8545779 -0.02969498
Seq191  0.8545779 -0.02969498
Seq192  1.1643475 -0.85457803
Seq193  1.1643475 -0.85457803
Seq194  1.1643475 -0.85457803
Seq195  1.1643475 -0.85457803
Seq196  1.1643475 -0.85457803
Seq220  1.2583084 -0.02969498
Seq221  0.1812273 -0.85457803
Seq222  1.2583084 -0.02969498
Seq223  1.1643475  1.04738615
Seq224  1.2583084  1.04738615
Seq225  1.2583084  0.95342528
Seq226  1.1643475 -1.22634782
Seq227  1.2583084  1.04738615
Seq228  1.2583084  0.65280643
Seq229  1.2583084  0.65280643
Seq264 -1.0154256 -1.22634782
Seq265 -1.0154256 -1.22634782
Seq266 -1.0154256 -1.22634782
Seq267 -1.0154256 -0.97634616
Seq268 -1.3132192 -0.97634616
Seq269 -1.0154256 -1.52414140
Seq270 -1.0154256 -1.52414140
Seq271 -1.0154256 -1.52414140
Seq272 -1.0154256 -0.97634616
Seq273 -1.0154256 -0.97634616
         [,1]     [,2]     [,3]     [,4]     [,5]
[1,] 0.000000 4.322655 5.137720 5.502178 5.066090
[2,] 4.322655 0.000000 4.320258 5.853720 4.088945
[3,] 5.137720 4.320258 0.000000 6.381773 4.585777
[4,] 5.502178 5.853720 6.381773 0.000000 6.913510
[5,] 5.066090 4.088945 4.585777 6.913510 0.000000

HDMD documentation built on May 1, 2019, 8:48 p.m.