WeightedGeneScore: Computation of weighted gene score of genes in Gene...
In dhga: Differential Hub Gene Analysis

Description Usage Arguments Value Author(s) Examples

View source: R/dhga.R

The function computes the weighted gene scores of all genes in a Gene Co-expression Network

1	WeightedGeneScore(x, beta, plot=TRUE)

`x`	x is a data frame of gene expression values where rows represent genes and columns represent samples/time points under a particular condition/stress/trait.
`beta`	beta is a soft threshold parameter determined from the scale free property of biological networks (Gene Co-expression Network).
`plot`	plot is a character must either take logical value TRUE/FALSE representing whether the plot of the gene connection degrees of all genes in Gene Co-expression Network needs to be constructed or not.

The function returns a vector of weighted gene scores of genes (nodes) in the Gene Co-expression Network along with the gene connectivity plot.

Samarendra Das and Baidya Nath Mandal

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3

data(rice_normal)
beta=6
WeightedGeneScore(rice_normal, beta, plot=FALSE)

Loading required package: VennDiagram
Loading required package: grid
Loading required package: futile.logger
                               WGS
Os.9805.1.S1_at          2.7328957
Os.8149.1.S1_at          8.8093517
Os.51343.1.S1_at        25.7210489
Os.2881.1.S1_at         10.0258620
Os.55524.1.S1_at        14.2737172
Os.22029.1.S1_a_at      16.0661082
OsAffx.3191.1.A1_at      0.3573509
OsAffx.12383.1.S1_at    17.3036480
Os.52157.1.S1_x_at       2.9918486
Os.26770.2.S1_x_at      22.2458184
Os.5140.1.S1_at          7.9274550
Os.2128.1.S1_at         27.5646639
Os.25613.1.A1_at        39.9928913
Os.32686.1.S1_at        13.3622213
OsAffx.27459.3.S1_at    16.1229823
Os.10487.1.S1_at         1.2226265
Os.31191.1.S1_at        39.4993271
Os.53177.1.S1_at         2.2654294
Os.40338.1.S1_at        15.9849336
Os.31171.1.S1_at        24.6955068
OsAffx.25039.1.S1_at    28.3424459
OsAffx.12783.1.S1_at    34.6993690
Os.47413.1.S1_at        27.7101376
Os.38638.4.S1_s_at       3.1052945
Os.4819.1.A1_s_at       31.6052323
Os.33971.1.S1_at         0.5838764
Os.18955.1.S1_at         4.3074994
Os.30269.1.S1_at         0.8820790
Os.38812.1.S1_at         9.1338737
Os.49650.1.S1_at         3.5491516
OsAffx.27459.3.S1_x_at  16.3063713
OsAffx.28409.1.S1_at    19.7344966
Os.11151.1.S1_a_at       3.4874475
Os.26511.1.S1_at         6.8460767
Os.41199.1.A1_at        10.5063343
Os.40007.1.S1_x_at       2.9480491
Os.10389.1.S1_at        18.8108089
OsAffx.20682.1.S1_at     0.6826932
Os.11272.1.S1_at        37.9146031
Os.9445.1.S1_at          1.7707209
Os.48215.1.A1_at         5.1222152
Os.8673.1.S1_at          4.6362681
Os.1465.1.S1_at          1.3655417
Os.53177.1.S1_s_at       0.9661417
OsAffx.28409.2.S1_s_at  24.3584869
Os.53439.1.S1_at        31.7847184
Os.12629.1.S1_at        32.1101735
Os.11555.1.S1_at        30.2829866
Os.11898.1.S1_at         0.6854787
Os.56232.1.S1_at        15.0621566
OsAffx.20930.1.S1_at     0.1988653
Os.47737.1.S1_at         6.0619038
OsAffx.17611.1.S1_at     3.4431111
Os.38638.3.S1_x_at      15.7701047
Os.52100.1.S1_at         0.7643040
Os.7770.1.S1_at          3.9362430
Os.9836.1.S1_at          5.3278674
Os.16744.1.S1_at         4.4266848
Os.51307.1.S1_at        23.8363221
OsAffx.26317.1.S2_at     0.4985639
OsAffx.2166.1.S1_at     28.9761330
Os.5621.1.S1_at          0.5702256
Os.11787.1.S1_at         1.1231757
Os.33625.4.S1_at         8.2313422
OsAffx.31756.4.S1_at    25.1525884
Os.50805.1.S1_at        14.2010080
OsAffx.29448.1.S1_at    31.0009955
Os.11801.1.S1_at         5.7224910
Os.47802.1.A1_at         1.1285630
OsAffx.18861.1.S1_at    26.5662111
Os.56150.1.S1_at         0.9247125
Os.12642.1.S1_at         1.8517116
Os.10469.1.S1_at        19.3504711
Os.55079.1.S1_at        27.2747665
Os.34174.1.S1_at         0.9504456
OsAffx.12433.1.S1_at    32.6441765
Os.50369.1.S1_at        10.9905752
OsAffx.15447.1.S1_at     2.3420625
Os.52619.1.S1_at         2.1067323
Os.17102.1.S1_at        31.0423392
OsAffx.30295.1.S1_at    14.7030544
Os.11800.1.S1_s_at       6.1310737
Os.10654.1.S1_s_at      36.7631411
Os.54579.1.S1_s_at      40.2545796
OsAffx.3569.1.S1_at     15.5260236
Os.55907.1.S1_at        40.2033072
Os.52058.1.S1_at         1.5208487
Os.57456.1.S1_x_at       1.6192015
Os.155.1.S1_a_at        12.8453576
Os.6345.1.S1_at          9.7321750
Os.11677.1.S1_x_at      30.5345194
OsAffx.8061.1.S1_at      0.8013865
OsAffx.13662.1.S1_at     6.2839978
Os.15199.1.S1_at         0.0738917
Os.31778.2.S1_x_at      20.0615313
Os.39994.1.S1_at         2.7622797
Os.50372.1.S1_at         0.9987358
Os.18381.1.S1_at         3.1692532
Os.11796.1.S1_at         2.3928201
OsAffx.19632.1.S1_at    26.3289404
Os.12767.1.S1_a_at      28.2431067
Os.34061.1.S1_a_at       0.7504656
Os.12239.1.S1_at         3.5159342
Os.49780.1.S1_x_at      10.4303614
OsAffx.7332.1.S1_at     16.1481891
Os.36162.1.S1_s_at      28.0881065
Os.44475.1.S1_at         6.2913011
Os.54555.1.S1_at        32.7413599
Os.15247.1.S1_s_at       7.8149272
Os.6683.1.S1_at         14.5924603
Os.56924.1.S1_at        29.5044907
OsAffx.15530.1.S1_at    39.7864171
Os.50290.1.S1_at        18.9503851
Os.57362.1.S1_at         0.2154498
Os.50883.1.S1_at        34.2297678
Os.12286.1.S1_at         1.5067558
Os.52536.1.S1_at        10.8276901
Os.6792.1.S1_at         18.9724708
Os.319.1.A1_at           4.6886197
Os.18933.1.S1_at         8.0590003
Os.4760.1.S1_at         18.0304364
OsAffx.30721.5.S1_at     1.0284667
OsAffx.15125.1.S1_at     2.7492409
Os.26802.1.S1_at         0.6471168
Os.11786.2.S1_at        16.6315918
Os.47413.1.S1_x_at      37.5752356
Os.24906.1.S1_at        10.4603609
Os.4715.1.S1_at          6.3280017
Os.534.2.S1_x_at        40.7065139
Os.8118.1.S1_at         32.2556765
Os.21319.1.S1_at        15.8735508
Os.23183.1.S1_at         1.2284527
Os.27659.1.S1_x_at       1.2134748
Os.23381.1.A1_at         2.6837515
Os.27759.1.S1_at         7.7103129
OsAffx.7934.1.S1_at     29.9952572
Os.54672.1.S1_at        42.0989110
Os.15471.1.S1_at        21.1255147
Os.31778.2.S1_at        27.0314724
Os.17652.1.S1_s_at      29.9414693
OsAffx.11963.1.S1_at    27.6188146
OsAffx.27299.1.S1_at     7.1451300
Os.5197.2.S1_x_at       29.0749826
Os.54653.1.S1_at        42.0458838
Os.16558.1.S1_at        22.5583081
Os.35154.1.S1_x_at      21.1474320
Os.54178.1.S1_at        20.9750178
Os.46710.2.S1_at         1.4671864
Os.54318.1.S1_at        34.5558594
OsAffx.13338.1.S1_at    19.3021850
Os.46869.1.A1_at        17.6618572
Os.44475.1.S1_x_at      18.2875144
Os.17997.1.S1_at        18.1034271
Os.32964.1.S1_at         2.7979861
Os.49294.1.S1_at         4.8301049
Os.26171.1.S1_at         3.6193734
Os.50450.1.S1_at         0.8281201
OsAffx.19332.1.S1_at    12.8415672
OsAffx.28727.1.S1_at    30.6648031
Os.16904.1.S1_at         1.0826054
Os.6825.1.S1_at         12.0714029
OsAffx.3504.1.S1_at     11.8517091
Os.4415.1.S1_at         25.3427000
Os.11834.1.S1_at         8.7020545
Os.37255.1.A1_at         8.0108495
Os.7674.1.S1_at          2.8965487
Os.56048.1.S1_s_at      26.5311229
OsAffx.15785.1.S1_at    10.4152485
Os.27624.1.S1_at         1.5364587
OsAffx.29866.1.S1_at     8.8593145
OsAffx.3569.1.S1_x_at   18.5639651
Os.6318.1.S1_at          1.7789136
OsAffx.27557.1.S1_at    25.9176486
Os.1479.1.S1_at         22.2703786
OsAffx.24515.1.S1_at    21.4561314
Os.51295.1.S1_at        11.1808211
Os.11255.1.S1_at        43.6312053
OsAffx.31756.4.S1_x_at  24.4865078
Os.49226.1.S1_at        20.0371255
OsAffx.17724.1.S1_at     9.8532278
OsAffx.3755.1.S1_at      6.1901818
Os.18664.1.S1_a_at       5.3874451
Os.33087.1.S1_at         1.4451340
Os.54146.1.S1_at        22.0895884
Os.11312.1.S1_s_at       3.9329737
OsAffx.4923.1.S1_at      6.3832116
OsAffx.29954.1.S1_at    15.0385510
OsAffx.27508.10.S1_s_at  1.4017825
Os.64.1.S1_at            1.2558351
OsAffx.30868.1.S1_at    21.4854484
Os.12986.1.S1_at        35.7447398
Os.52151.1.S1_at        18.7155463
OsAffx.31107.1.S1_at     9.5786484
Os.51491.1.S1_at         1.8317409
Os.11144.1.S1_at         4.0154300
Os.11308.1.S1_at        10.7291339
Os.40000.1.S1_at        41.3382048
Os.11251.1.S1_at        35.4221952
Os.5510.1.S1_at          0.6356982
Os.18830.1.S1_at         7.9473404