DiffHub: Differential Hub status of the genes in a gene co-expression...
In dhga: Differential Hub Gene Analysis
Description
Usage
Arguments
Value
Author(s)
Examples
Description
The function returns hub status of each gene in a gene co-expression network under two contrasting conditions
Usage
1
Arguments
x
x is a data frame of gene expression values where rows represent genes and columns represent samples/time point under stress condition.
y
y is a data frame of gene expression values where rows represent genes and columns represent samples/time points under control condition.
m1
m1 is a scalar representing sample size and is less than or equal to number of columns in x.
m2
m2 is a scalar representing sample size and is less than or equal to number of columns in y.
s
s is a scalar representing number of times each of the m samples will be resampled.
beta
beta is a soft threshold parameter determined from the scale free property of biological networks (GCN).
alpha
alpha is a scalar representing statistical level of significance. Default is alpha=0.0001
plot
plot is a character representing whether the hubplot can be drawn (TRUE) or not (FALSE).
Value
The function returns a list with two components. First component returns the list of genes along with their hub status. Second component gives a table containing number of genes under different categories of hubs viz. housekeeping, unique to stress and unique to normal. The function also returns a venn plot of hub genes and unique hub genes under two conditions.
Author(s)
Samarendra Das and Baidya Nath Mandal
Examples
1
2
3
data(rice_salt)
data(rice_normal)
DiffHub(rice_salt,rice_normal,18,18,80, 6, alpha=0.0001, plot=TRUE)
Example output
Loading required package: VennDiagram
Loading required package: grid
Loading required package: futile.logger
Genes pval_stres pval_control
1 Os.9805.1.S1_at 0.941604451533238 0.999999999999664
2 Os.8149.1.S1_at 4.63444571122451e-05 0.999681038985433
3 Os.51343.1.S1_at 3.92476327401578e-15 4.39269420205013e-12
4 Os.2881.1.S1_at 0.999999845307515 0.723991230418568
5 Os.55524.1.S1_at 3.92476327401578e-15 5.87177790874301e-05
6 Os.22029.1.S1_a_at 3.92476327401578e-15 3.7150926354495e-07
7 OsAffx.3191.1.A1_at 0.999999999999903 0.999999999999978
8 OsAffx.12383.1.S1_at 3.92476327401578e-15 7.72400144649286e-08
9 Os.52157.1.S1_x_at 7.9859085208918e-12 0.999999999999994
10 Os.26770.2.S1_x_at 3.92476327401578e-15 3.15715405812253e-14
11 Os.5140.1.S1_at 0.992182555368699 0.999186885019411
12 Os.2128.1.S1_at 8.81719931069549e-05 1.8463116486971e-13
13 Os.25613.1.A1_at 3.92476327401578e-15 5.11311585323595e-15
14 Os.32686.1.S1_at 7.4160715100999e-05 0.112476873271489
15 OsAffx.27459.3.S1_at 3.92476327401578e-15 6.31242983607681e-10
16 Os.10487.1.S1_at 0.999999974613545 0.999999999999996
17 Os.31191.1.S1_at 3.92476327401578e-15 7.73081088874527e-15
18 Os.53177.1.S1_at 0.99999999999947 0.999999999998404
19 Os.40338.1.S1_at 0.999998701492955 1.97469327145533e-06
20 Os.31171.1.S1_at 0.999994661585973 9.22353211695756e-13
21 OsAffx.25039.1.S1_at 3.92476327401578e-15 1.34027548914676e-13
22 OsAffx.12783.1.S1_at 3.92476327401578e-15 1.12307783232509e-14
23 Os.47413.1.S1_at 3.92476327401578e-15 2.26908960996523e-14
24 Os.38638.4.S1_s_at 1.28464005847853e-09 0.999999999999996
25 Os.4819.1.A1_s_at 5.27439293354229e-10 1.16566630081387e-14
26 Os.33971.1.S1_at 4.23334128259882e-15 0.999999999999996
27 Os.18955.1.S1_at 1.20984237823333e-14 0.999999999999972
28 Os.30269.1.S1_at 0.999999999999962 0.999999999999996
29 Os.38812.1.S1_at 0.00232878677282802 0.9908569470318
30 Os.49650.1.S1_at 0.999999999999925 0.999999999997681
31 OsAffx.27459.3.S1_x_at 3.92476327401578e-15 7.85853897097708e-11
32 OsAffx.28409.1.S1_at 8.08167496805292e-07 4.17454208077212e-11
33 Os.11151.1.S1_a_at 0.888436827383207 0.975926593484629
34 Os.26511.1.S1_at 0.999973644580776 0.999999364546065
35 Os.41199.1.A1_at 0.237413661845626 0.305584167848551
36 Os.40007.1.S1_x_at 4.00184648825297e-08 0.999999999999937
37 Os.10389.1.S1_at 3.92476327401578e-15 2.16700023312062e-12
38 OsAffx.20682.1.S1_at 0.000592866196309347 0.999999999999996
39 Os.11272.1.S1_at 3.92476327401578e-15 4.92385029896428e-15
40 Os.9445.1.S1_at 0.994856260982103 0.999999999997758
41 Os.48215.1.A1_at 2.05802385119303e-10 0.999999547853571
42 Os.8673.1.S1_at 0.995946137898571 0.999999999998608
43 Os.1465.1.S1_at 0.99999911080231 0.99999999999999
44 Os.53177.1.S1_s_at 0.999999841326262 0.999999999999985
45 OsAffx.28409.2.S1_s_at 5.60040631520097e-10 1.60168141988126e-13
46 Os.53439.1.S1_at 0.999999999999987 3.93081720930364e-14
47 Os.12629.1.S1_at 4.54720281154268e-14 5.94443277980381e-15
48 Os.11555.1.S1_at 3.92476327401578e-15 3.39675415987301e-14
49 Os.11898.1.S1_at 0.999999988171485 0.999999999999996
50 Os.56232.1.S1_at 0.997048026058994 0.000712519313599594
51 OsAffx.20930.1.S1_at 0.99999999871536 0.999999999999996
52 Os.47737.1.S1_at 3.92476327401578e-15 0.9999994090227
53 OsAffx.17611.1.S1_at 2.03170187061123e-14 0.999999997343844
54 Os.38638.3.S1_x_at 6.30242576336997e-14 5.64311920954829e-08
55 Os.52100.1.S1_at 0.99999999999999 0.999999999999996
56 Os.7770.1.S1_at 0.999999619226138 0.999999930408472
57 Os.9836.1.S1_at 0.950028137336724 0.999999961031733
58 Os.16744.1.S1_at 0.39043530601405 0.999999999572732
59 Os.51307.1.S1_at 3.92476327401578e-15 4.94320300617142e-13
60 OsAffx.26317.1.S2_at 3.92476327401578e-15 0.999999999999994
61 OsAffx.2166.1.S1_at 0.99998587658498 2.44228833203713e-14
62 Os.5621.1.S1_at 0.99999999999999 0.999999999999996
63 Os.11787.1.S1_at 0.000297216758809992 0.999999999999996
64 Os.33625.4.S1_at 0.999967694794693 0.996778016170526
65 OsAffx.31756.4.S1_at 5.51337716307303e-15 4.10857571561029e-12
66 Os.50805.1.S1_at 0.815115382178675 4.72731332921029e-05
67 OsAffx.29448.1.S1_at 4.92385029896428e-15 2.82858698794875e-14
68 Os.11801.1.S1_at 1.8463116486971e-13 0.999796007196714
69 Os.47802.1.A1_at 0.00684508903823154 0.999999999993231
70 OsAffx.18861.1.S1_at 0.0540539289192386 2.36566077953247e-13
71 Os.56150.1.S1_at 0.999999999999978 0.999999999999995
72 Os.12642.1.S1_at 0.99999857383247 0.999999999999991
73 Os.10469.1.S1_at 0.999999983999331 5.11848264049335e-13
74 Os.55079.1.S1_at 0.999663769491182 1.35248806585821e-14
75 Os.34174.1.S1_at 0.999999999999996 0.999999999999996
76 OsAffx.12433.1.S1_at 3.92476327401578e-15 2.44228833203713e-14
77 Os.50369.1.S1_at 0.136025894125641 0.0984903953145205
78 OsAffx.15447.1.S1_at 0.707733937489629 0.99999999999999
79 Os.52619.1.S1_at 0.888436827383207 0.999999999999982
80 Os.17102.1.S1_at 3.92476327401578e-15 2.03170187061123e-14
81 OsAffx.30295.1.S1_at 7.73081088874527e-15 1.26834873586762e-06
82 Os.11800.1.S1_s_at 0.999999983999331 0.999999998423378
83 Os.10654.1.S1_s_at 5.11311585323595e-15 5.11311585323595e-15
84 Os.54579.1.S1_s_at 3.92476327401578e-15 4.92385029896428e-15
85 OsAffx.3569.1.S1_at 0.000483690195025385 8.81719931069549e-05
86 Os.55907.1.S1_at 3.92476327401578e-15 5.30953621332251e-15
87 Os.52058.1.S1_at 0.999999999997346 0.999999999999992
88 Os.57456.1.S1_x_at 4.39646307568141e-15 0.999999995298373
89 Os.155.1.S1_a_at 0.999922919986431 2.47835388695014e-05
90 Os.6345.1.S1_at 0.998172807771626 0.988059901999347
91 Os.11677.1.S1_x_at 4.07617944015762e-15 7.17249171681204e-15
92 OsAffx.8061.1.S1_at 0.0416849054406589 0.999999999999991
93 OsAffx.13662.1.S1_at 0.999999987840749 0.999999762445716
94 Os.15199.1.S1_at 0.999999942066096 0.999999999999996
95 Os.31778.2.S1_x_at 6.43413454729558e-08 6.70079822294117e-10
96 Os.39994.1.S1_at 0.955686198030694 0.999999999999958
97 Os.50372.1.S1_at 0.999999999222356 0.999999999988534
98 Os.18381.1.S1_at 0.999999999996284 0.999999999998043
99 Os.11796.1.S1_at 0.9999999685249 0.999999999999884
100 OsAffx.19632.1.S1_at 3.92476327401578e-15 3.87083016155488e-13
101 Os.12767.1.S1_a_at 0.99999997320822 8.97877318402061e-15
102 Os.34061.1.S1_a_at 0.999891320774406 0.999999999999996
103 Os.12239.1.S1_at 0.937584980750844 0.99999999999999
104 Os.49780.1.S1_x_at 4.45000781663778e-08 0.240388248212199
105 OsAffx.7332.1.S1_at 3.92476327401578e-15 5.9609774488797e-06
106 Os.36162.1.S1_s_at 0.665262831041251 2.28351421165582e-13
107 Os.44475.1.S1_at 0.975100209262415 0.999999886162783
108 Os.54555.1.S1_at 3.20318418641634e-07 1.08202086145047e-14
109 Os.15247.1.S1_s_at 0.315745710669308 0.999992079551751
110 Os.6683.1.S1_at 0.995525240663573 2.06792882870972e-06
111 Os.56924.1.S1_at 6.17222887962025e-15 2.93418920032662e-14
112 OsAffx.15530.1.S1_at 4.00871895024803e-13 6.65389147686702e-15
113 Os.50290.1.S1_at 4.23334128259882e-15 1.39502405225593e-11
114 Os.57362.1.S1_at 0.999999999986498 0.999999999999996
115 Os.50883.1.S1_at 1.99447481476309e-11 4.39646307568141e-15
116 Os.12286.1.S1_at 0.999999999999686 0.999999999999988
117 Os.52536.1.S1_at 0.494259872822906 0.0461394787327262
118 Os.6792.1.S1_at 5.11311585323595e-15 3.59753367465694e-08
119 Os.319.1.A1_at 0.999999999999993 0.999999999781172
120 Os.18933.1.S1_at 0.999556043746201 0.992284979711702
121 Os.4760.1.S1_at 0.542017732357546 4.00871895024803e-13
122 OsAffx.30721.5.S1_at 0.968962224823886 0.999999999999996
123 OsAffx.15125.1.S1_at 0.999999824389027 0.999999999999737
124 Os.26802.1.S1_at 0.999975720370849 0.999999999999996
125 Os.11786.2.S1_at 0.999999999994453 2.24166102489321e-12
126 Os.47413.1.S1_x_at 3.92476327401578e-15 9.32052548996272e-15
127 Os.24906.1.S1_at 0.125832907588746 0.477051369750925
128 Os.4715.1.S1_at 0.991868069567487 0.999999998328706
129 Os.534.2.S1_x_at 3.92476327401578e-15 5.11311585323595e-15
130 Os.8118.1.S1_at 1.30319196276126e-14 4.22798310401752e-14
131 Os.21319.1.S1_at 6.60149967075797e-05 1.39316779813774e-06
132 Os.23183.1.S1_at 1.32548257290976e-05 0.999999999999996
133 Os.27659.1.S1_x_at 0.999799678546418 0.999999999999993
134 Os.23381.1.A1_at 0.998384810871295 0.999999999999866
135 Os.27759.1.S1_at 0.99999999999947 0.90316417946214
136 OsAffx.7934.1.S1_at 9.67506653877832e-15 5.65381650012578e-14
137 Os.54672.1.S1_at 3.92476327401578e-15 3.92476327401578e-15
138 Os.15471.1.S1_at 0.581698414440978 2.65615551406177e-09
139 Os.31778.2.S1_at 5.10838635074007e-07 1.3889612535351e-13
140 Os.17652.1.S1_s_at 0.0154511215885179 9.67506653877832e-15
141 OsAffx.11963.1.S1_at 0.397817809904805 2.53369790186473e-14
142 OsAffx.27299.1.S1_at 0.0138504710992339 0.999999930408472
143 Os.5197.2.S1_x_at 3.92476327401578e-15 8.0257899988438e-15
144 Os.54653.1.S1_at 3.92476327401578e-15 3.92476327401578e-15
145 Os.16558.1.S1_at 0.347050602369086 1.21414887761266e-12
146 Os.35154.1.S1_x_at 5.30953621332251e-15 8.41107462030933e-14
147 Os.54178.1.S1_at 4.92385029896428e-15 1.60860855994897e-10
148 Os.46710.2.S1_at 0.999999999043055 0.99999999999925
149 Os.54318.1.S1_at 3.27480058990236e-14 8.33183570817745e-15
150 OsAffx.13338.1.S1_at 4.39646307568141e-15 9.56945150584442e-10
151 Os.46869.1.A1_at 0.807337862876547 6.09057043796986e-13
152 Os.44475.1.S1_x_at 0.862924569208568 6.31242983607681e-10
153 Os.17997.1.S1_at 0.701108584708885 1.43404313022749e-08
154 Os.32964.1.S1_at 3.65376652789413e-06 0.999999999999989
155 Os.49294.1.S1_at 5.3538105508122e-08 0.99999999999993
156 Os.26171.1.S1_at 0.999999991279402 0.999999999981307
157 Os.50450.1.S1_at 0.999999999693809 0.999999999999994
158 OsAffx.19332.1.S1_at 7.44650475049233e-15 0.232989926829363
159 OsAffx.28727.1.S1_at 6.33502828108896e-12 1.30319196276126e-14
160 Os.16904.1.S1_at 0.999999999999996 0.999999999999996
161 Os.6825.1.S1_at 0.0087944119683183 0.227163492847201
162 OsAffx.3504.1.S1_at 0.714290155730357 0.0117917462590248
163 Os.4415.1.S1_at 3.93081720930364e-14 3.7158508920231e-12
164 Os.11834.1.S1_at 4.03102420786909e-05 0.99969748042776
165 Os.37255.1.A1_at 0.408959717155736 0.999992896581193
166 Os.7674.1.S1_at 0.999999999999626 0.999799678546418
167 Os.56048.1.S1_s_at 3.92476327401578e-15 4.39269420205013e-12
168 OsAffx.15785.1.S1_at 0.11807141577282 0.384924078726979
169 Os.27624.1.S1_at 4.04361222716952e-11 0.999999999999996
170 OsAffx.29866.1.S1_at 5.30953621332251e-15 0.792569387556402
171 OsAffx.3569.1.S1_x_at 0.0272204916784457 1.89445815950918e-07
172 Os.6318.1.S1_at 0.24943255693902 0.999999999999996
173 OsAffx.27557.1.S1_at 3.92476327401578e-15 4.89008147727872e-14
174 Os.1479.1.S1_at 0.11432028443542 1.59594850002947e-12
175 OsAffx.24515.1.S1_at 3.92476327401578e-15 2.50037606489293e-11
176 Os.51295.1.S1_at 0.999927259590046 0.155765058812464
177 Os.11255.1.S1_at 9.54670346713074e-13 5.11311585323595e-15
178 OsAffx.31756.4.S1_x_at 4.39646307568141e-15 2.02491863866523e-12
179 Os.49226.1.S1_at 0.999999999999994 1.18474072609428e-11
180 OsAffx.17724.1.S1_at 0.0141932467963315 0.730367476362221
181 OsAffx.3755.1.S1_at 0.999999999999993 0.999999394540815
182 Os.18664.1.S1_a_at 0.998995196883764 0.99999999763306
183 Os.33087.1.S1_at 8.09426644968574e-06 0.999999999999994
184 Os.54146.1.S1_at 3.92476327401578e-15 1.71103540371855e-10
185 Os.11312.1.S1_s_at 3.92476327401578e-15 0.999999999999896
186 OsAffx.4923.1.S1_at 0.000348222211294648 0.999998397264933
187 OsAffx.29954.1.S1_at 7.23234617567231e-12 1.16798228595587e-07
188 OsAffx.27508.10.S1_s_at 0.302229477672359 0.999999999999973
189 Os.64.1.S1_at 4.07673948865954e-14 0.999999999999994
190 OsAffx.30868.1.S1_at 3.92476327401578e-15 5.94753040972601e-08
191 Os.12986.1.S1_at 0.816392402760777 1.95813709440537e-14
192 Os.52151.1.S1_at 1.92959981469297e-06 4.541884742328e-12
193 OsAffx.31107.1.S1_at 0.999999999999958 0.727188594229806
194 Os.51491.1.S1_at 6.10611894103502e-05 0.999999999999995
195 Os.11144.1.S1_at 2.50749348108444e-09 0.999999999987352
196 Os.11308.1.S1_at 5.30953621332251e-15 0.837255056899589
197 Os.40000.1.S1_at 3.92476327401578e-15 6.65389147686702e-15
198 Os.11251.1.S1_at 1.88719325968143e-14 7.44650475049233e-15
199 Os.5510.1.S1_at 0.457982267642454 0.999999999999996
200 Os.18830.1.S1_at 0.101861459454507 0.999620037752728
HubStatus
1 Not Hub
2 Unique Hub to Stress
3 Housekeeping Hub
4 Not Hub
5 Housekeeping Hub
6 Housekeeping Hub
7 Not Hub
8 Housekeeping Hub
9 Unique Hub to Stress
10 Housekeeping Hub
11 Not Hub
12 Housekeeping Hub
13 Housekeeping Hub
14 Unique Hub to Stress
15 Housekeeping Hub
16 Not Hub
17 Housekeeping Hub
18 Not Hub
19 Unique Hub to Normal
20 Unique Hub to Normal
21 Housekeeping Hub
22 Housekeeping Hub
23 Housekeeping Hub
24 Unique Hub to Stress
25 Housekeeping Hub
26 Unique Hub to Stress
27 Unique Hub to Stress
28 Not Hub
29 Not Hub
30 Not Hub
31 Housekeeping Hub
32 Housekeeping Hub
33 Not Hub
34 Not Hub
35 Not Hub
36 Unique Hub to Stress
37 Housekeeping Hub
38 Not Hub
39 Housekeeping Hub
40 Not Hub
41 Unique Hub to Stress
42 Not Hub
43 Not Hub
44 Not Hub
45 Housekeeping Hub
46 Unique Hub to Normal
47 Housekeeping Hub
48 Housekeeping Hub
49 Not Hub
50 Not Hub
51 Not Hub
52 Unique Hub to Stress
53 Unique Hub to Stress
54 Housekeeping Hub
55 Not Hub
56 Not Hub
57 Not Hub
58 Not Hub
59 Housekeeping Hub
60 Unique Hub to Stress
61 Unique Hub to Normal
62 Not Hub
63 Not Hub
64 Not Hub
65 Housekeeping Hub
66 Unique Hub to Normal
67 Housekeeping Hub
68 Unique Hub to Stress
69 Not Hub
70 Unique Hub to Normal
71 Not Hub
72 Not Hub
73 Unique Hub to Normal
74 Unique Hub to Normal
75 Not Hub
76 Housekeeping Hub
77 Not Hub
78 Not Hub
79 Not Hub
80 Housekeeping Hub
81 Housekeeping Hub
82 Not Hub
83 Housekeeping Hub
84 Housekeeping Hub
85 Unique Hub to Normal
86 Housekeeping Hub
87 Not Hub
88 Unique Hub to Stress
89 Unique Hub to Normal
90 Not Hub
91 Housekeeping Hub
92 Not Hub
93 Not Hub
94 Not Hub
95 Housekeeping Hub
96 Not Hub
97 Not Hub
98 Not Hub
99 Not Hub
100 Housekeeping Hub
101 Unique Hub to Normal
102 Not Hub
103 Not Hub
104 Unique Hub to Stress
105 Housekeeping Hub
106 Unique Hub to Normal
107 Not Hub
108 Housekeeping Hub
109 Not Hub
110 Unique Hub to Normal
111 Housekeeping Hub
112 Housekeeping Hub
113 Housekeeping Hub
114 Not Hub
115 Housekeeping Hub
116 Not Hub
117 Not Hub
118 Housekeeping Hub
119 Not Hub
120 Not Hub
121 Unique Hub to Normal
122 Not Hub
123 Not Hub
124 Not Hub
125 Unique Hub to Normal
126 Housekeeping Hub
127 Not Hub
128 Not Hub
129 Housekeeping Hub
130 Housekeeping Hub
131 Housekeeping Hub
132 Unique Hub to Stress
133 Not Hub
134 Not Hub
135 Not Hub
136 Housekeeping Hub
137 Housekeeping Hub
138 Unique Hub to Normal
139 Housekeeping Hub
140 Unique Hub to Normal
141 Unique Hub to Normal
142 Not Hub
143 Housekeeping Hub
144 Housekeeping Hub
145 Unique Hub to Normal
146 Housekeeping Hub
147 Housekeeping Hub
148 Not Hub
149 Housekeeping Hub
150 Housekeeping Hub
151 Unique Hub to Normal
152 Unique Hub to Normal
153 Unique Hub to Normal
154 Unique Hub to Stress
155 Unique Hub to Stress
156 Not Hub
157 Not Hub
158 Unique Hub to Stress
159 Housekeeping Hub
160 Not Hub
161 Not Hub
162 Not Hub
163 Housekeeping Hub
164 Unique Hub to Stress
165 Not Hub
166 Not Hub
167 Housekeeping Hub
168 Not Hub
169 Unique Hub to Stress
170 Unique Hub to Stress
171 Unique Hub to Normal
172 Not Hub
173 Housekeeping Hub
174 Unique Hub to Normal
175 Housekeeping Hub
176 Not Hub
177 Housekeeping Hub
178 Housekeeping Hub
179 Unique Hub to Normal
180 Not Hub
181 Not Hub
182 Not Hub
183 Unique Hub to Stress
184 Housekeeping Hub
185 Unique Hub to Stress
186 Not Hub
187 Housekeeping Hub
188 Not Hub
189 Unique Hub to Stress
190 Housekeeping Hub
191 Unique Hub to Normal
192 Housekeeping Hub
193 Not Hub
194 Unique Hub to Stress
195 Unique Hub to Stress
196 Unique Hub to Stress
197 Housekeeping Hub
198 Housekeeping Hub
199 Not Hub
200 Not Hub
dhga documentation built on May 2, 2019, 2:13 p.m.
R Package Documentation
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Description Usage Arguments Value Author(s) Examples
Description
The function returns hub status of each gene in a gene co-expression network under two contrasting conditions
Usage
1 |
Arguments
x |
x is a data frame of gene expression values where rows represent genes and columns represent samples/time point under stress condition. |
y |
y is a data frame of gene expression values where rows represent genes and columns represent samples/time points under control condition. |
m1 |
m1 is a scalar representing sample size and is less than or equal to number of columns in x. |
m2 |
m2 is a scalar representing sample size and is less than or equal to number of columns in y. |
s |
s is a scalar representing number of times each of the m samples will be resampled. |
beta |
beta is a soft threshold parameter determined from the scale free property of biological networks (GCN). |
alpha |
alpha is a scalar representing statistical level of significance. Default is alpha=0.0001 |
plot |
plot is a character representing whether the hubplot can be drawn (TRUE) or not (FALSE). |
Value
The function returns a list with two components. First component returns the list of genes along with their hub status. Second component gives a table containing number of genes under different categories of hubs viz. housekeeping, unique to stress and unique to normal. The function also returns a venn plot of hub genes and unique hub genes under two conditions.
Author(s)
Samarendra Das and Baidya Nath Mandal
Examples
1 2 3 | data(rice_salt)
data(rice_normal)
DiffHub(rice_salt,rice_normal,18,18,80, 6, alpha=0.0001, plot=TRUE)
|
Example output
Loading required package: VennDiagram
Loading required package: grid
Loading required package: futile.logger
Genes pval_stres pval_control
1 Os.9805.1.S1_at 0.941604451533238 0.999999999999664
2 Os.8149.1.S1_at 4.63444571122451e-05 0.999681038985433
3 Os.51343.1.S1_at 3.92476327401578e-15 4.39269420205013e-12
4 Os.2881.1.S1_at 0.999999845307515 0.723991230418568
5 Os.55524.1.S1_at 3.92476327401578e-15 5.87177790874301e-05
6 Os.22029.1.S1_a_at 3.92476327401578e-15 3.7150926354495e-07
7 OsAffx.3191.1.A1_at 0.999999999999903 0.999999999999978
8 OsAffx.12383.1.S1_at 3.92476327401578e-15 7.72400144649286e-08
9 Os.52157.1.S1_x_at 7.9859085208918e-12 0.999999999999994
10 Os.26770.2.S1_x_at 3.92476327401578e-15 3.15715405812253e-14
11 Os.5140.1.S1_at 0.992182555368699 0.999186885019411
12 Os.2128.1.S1_at 8.81719931069549e-05 1.8463116486971e-13
13 Os.25613.1.A1_at 3.92476327401578e-15 5.11311585323595e-15
14 Os.32686.1.S1_at 7.4160715100999e-05 0.112476873271489
15 OsAffx.27459.3.S1_at 3.92476327401578e-15 6.31242983607681e-10
16 Os.10487.1.S1_at 0.999999974613545 0.999999999999996
17 Os.31191.1.S1_at 3.92476327401578e-15 7.73081088874527e-15
18 Os.53177.1.S1_at 0.99999999999947 0.999999999998404
19 Os.40338.1.S1_at 0.999998701492955 1.97469327145533e-06
20 Os.31171.1.S1_at 0.999994661585973 9.22353211695756e-13
21 OsAffx.25039.1.S1_at 3.92476327401578e-15 1.34027548914676e-13
22 OsAffx.12783.1.S1_at 3.92476327401578e-15 1.12307783232509e-14
23 Os.47413.1.S1_at 3.92476327401578e-15 2.26908960996523e-14
24 Os.38638.4.S1_s_at 1.28464005847853e-09 0.999999999999996
25 Os.4819.1.A1_s_at 5.27439293354229e-10 1.16566630081387e-14
26 Os.33971.1.S1_at 4.23334128259882e-15 0.999999999999996
27 Os.18955.1.S1_at 1.20984237823333e-14 0.999999999999972
28 Os.30269.1.S1_at 0.999999999999962 0.999999999999996
29 Os.38812.1.S1_at 0.00232878677282802 0.9908569470318
30 Os.49650.1.S1_at 0.999999999999925 0.999999999997681
31 OsAffx.27459.3.S1_x_at 3.92476327401578e-15 7.85853897097708e-11
32 OsAffx.28409.1.S1_at 8.08167496805292e-07 4.17454208077212e-11
33 Os.11151.1.S1_a_at 0.888436827383207 0.975926593484629
34 Os.26511.1.S1_at 0.999973644580776 0.999999364546065
35 Os.41199.1.A1_at 0.237413661845626 0.305584167848551
36 Os.40007.1.S1_x_at 4.00184648825297e-08 0.999999999999937
37 Os.10389.1.S1_at 3.92476327401578e-15 2.16700023312062e-12
38 OsAffx.20682.1.S1_at 0.000592866196309347 0.999999999999996
39 Os.11272.1.S1_at 3.92476327401578e-15 4.92385029896428e-15
40 Os.9445.1.S1_at 0.994856260982103 0.999999999997758
41 Os.48215.1.A1_at 2.05802385119303e-10 0.999999547853571
42 Os.8673.1.S1_at 0.995946137898571 0.999999999998608
43 Os.1465.1.S1_at 0.99999911080231 0.99999999999999
44 Os.53177.1.S1_s_at 0.999999841326262 0.999999999999985
45 OsAffx.28409.2.S1_s_at 5.60040631520097e-10 1.60168141988126e-13
46 Os.53439.1.S1_at 0.999999999999987 3.93081720930364e-14
47 Os.12629.1.S1_at 4.54720281154268e-14 5.94443277980381e-15
48 Os.11555.1.S1_at 3.92476327401578e-15 3.39675415987301e-14
49 Os.11898.1.S1_at 0.999999988171485 0.999999999999996
50 Os.56232.1.S1_at 0.997048026058994 0.000712519313599594
51 OsAffx.20930.1.S1_at 0.99999999871536 0.999999999999996
52 Os.47737.1.S1_at 3.92476327401578e-15 0.9999994090227
53 OsAffx.17611.1.S1_at 2.03170187061123e-14 0.999999997343844
54 Os.38638.3.S1_x_at 6.30242576336997e-14 5.64311920954829e-08
55 Os.52100.1.S1_at 0.99999999999999 0.999999999999996
56 Os.7770.1.S1_at 0.999999619226138 0.999999930408472
57 Os.9836.1.S1_at 0.950028137336724 0.999999961031733
58 Os.16744.1.S1_at 0.39043530601405 0.999999999572732
59 Os.51307.1.S1_at 3.92476327401578e-15 4.94320300617142e-13
60 OsAffx.26317.1.S2_at 3.92476327401578e-15 0.999999999999994
61 OsAffx.2166.1.S1_at 0.99998587658498 2.44228833203713e-14
62 Os.5621.1.S1_at 0.99999999999999 0.999999999999996
63 Os.11787.1.S1_at 0.000297216758809992 0.999999999999996
64 Os.33625.4.S1_at 0.999967694794693 0.996778016170526
65 OsAffx.31756.4.S1_at 5.51337716307303e-15 4.10857571561029e-12
66 Os.50805.1.S1_at 0.815115382178675 4.72731332921029e-05
67 OsAffx.29448.1.S1_at 4.92385029896428e-15 2.82858698794875e-14
68 Os.11801.1.S1_at 1.8463116486971e-13 0.999796007196714
69 Os.47802.1.A1_at 0.00684508903823154 0.999999999993231
70 OsAffx.18861.1.S1_at 0.0540539289192386 2.36566077953247e-13
71 Os.56150.1.S1_at 0.999999999999978 0.999999999999995
72 Os.12642.1.S1_at 0.99999857383247 0.999999999999991
73 Os.10469.1.S1_at 0.999999983999331 5.11848264049335e-13
74 Os.55079.1.S1_at 0.999663769491182 1.35248806585821e-14
75 Os.34174.1.S1_at 0.999999999999996 0.999999999999996
76 OsAffx.12433.1.S1_at 3.92476327401578e-15 2.44228833203713e-14
77 Os.50369.1.S1_at 0.136025894125641 0.0984903953145205
78 OsAffx.15447.1.S1_at 0.707733937489629 0.99999999999999
79 Os.52619.1.S1_at 0.888436827383207 0.999999999999982
80 Os.17102.1.S1_at 3.92476327401578e-15 2.03170187061123e-14
81 OsAffx.30295.1.S1_at 7.73081088874527e-15 1.26834873586762e-06
82 Os.11800.1.S1_s_at 0.999999983999331 0.999999998423378
83 Os.10654.1.S1_s_at 5.11311585323595e-15 5.11311585323595e-15
84 Os.54579.1.S1_s_at 3.92476327401578e-15 4.92385029896428e-15
85 OsAffx.3569.1.S1_at 0.000483690195025385 8.81719931069549e-05
86 Os.55907.1.S1_at 3.92476327401578e-15 5.30953621332251e-15
87 Os.52058.1.S1_at 0.999999999997346 0.999999999999992
88 Os.57456.1.S1_x_at 4.39646307568141e-15 0.999999995298373
89 Os.155.1.S1_a_at 0.999922919986431 2.47835388695014e-05
90 Os.6345.1.S1_at 0.998172807771626 0.988059901999347
91 Os.11677.1.S1_x_at 4.07617944015762e-15 7.17249171681204e-15
92 OsAffx.8061.1.S1_at 0.0416849054406589 0.999999999999991
93 OsAffx.13662.1.S1_at 0.999999987840749 0.999999762445716
94 Os.15199.1.S1_at 0.999999942066096 0.999999999999996
95 Os.31778.2.S1_x_at 6.43413454729558e-08 6.70079822294117e-10
96 Os.39994.1.S1_at 0.955686198030694 0.999999999999958
97 Os.50372.1.S1_at 0.999999999222356 0.999999999988534
98 Os.18381.1.S1_at 0.999999999996284 0.999999999998043
99 Os.11796.1.S1_at 0.9999999685249 0.999999999999884
100 OsAffx.19632.1.S1_at 3.92476327401578e-15 3.87083016155488e-13
101 Os.12767.1.S1_a_at 0.99999997320822 8.97877318402061e-15
102 Os.34061.1.S1_a_at 0.999891320774406 0.999999999999996
103 Os.12239.1.S1_at 0.937584980750844 0.99999999999999
104 Os.49780.1.S1_x_at 4.45000781663778e-08 0.240388248212199
105 OsAffx.7332.1.S1_at 3.92476327401578e-15 5.9609774488797e-06
106 Os.36162.1.S1_s_at 0.665262831041251 2.28351421165582e-13
107 Os.44475.1.S1_at 0.975100209262415 0.999999886162783
108 Os.54555.1.S1_at 3.20318418641634e-07 1.08202086145047e-14
109 Os.15247.1.S1_s_at 0.315745710669308 0.999992079551751
110 Os.6683.1.S1_at 0.995525240663573 2.06792882870972e-06
111 Os.56924.1.S1_at 6.17222887962025e-15 2.93418920032662e-14
112 OsAffx.15530.1.S1_at 4.00871895024803e-13 6.65389147686702e-15
113 Os.50290.1.S1_at 4.23334128259882e-15 1.39502405225593e-11
114 Os.57362.1.S1_at 0.999999999986498 0.999999999999996
115 Os.50883.1.S1_at 1.99447481476309e-11 4.39646307568141e-15
116 Os.12286.1.S1_at 0.999999999999686 0.999999999999988
117 Os.52536.1.S1_at 0.494259872822906 0.0461394787327262
118 Os.6792.1.S1_at 5.11311585323595e-15 3.59753367465694e-08
119 Os.319.1.A1_at 0.999999999999993 0.999999999781172
120 Os.18933.1.S1_at 0.999556043746201 0.992284979711702
121 Os.4760.1.S1_at 0.542017732357546 4.00871895024803e-13
122 OsAffx.30721.5.S1_at 0.968962224823886 0.999999999999996
123 OsAffx.15125.1.S1_at 0.999999824389027 0.999999999999737
124 Os.26802.1.S1_at 0.999975720370849 0.999999999999996
125 Os.11786.2.S1_at 0.999999999994453 2.24166102489321e-12
126 Os.47413.1.S1_x_at 3.92476327401578e-15 9.32052548996272e-15
127 Os.24906.1.S1_at 0.125832907588746 0.477051369750925
128 Os.4715.1.S1_at 0.991868069567487 0.999999998328706
129 Os.534.2.S1_x_at 3.92476327401578e-15 5.11311585323595e-15
130 Os.8118.1.S1_at 1.30319196276126e-14 4.22798310401752e-14
131 Os.21319.1.S1_at 6.60149967075797e-05 1.39316779813774e-06
132 Os.23183.1.S1_at 1.32548257290976e-05 0.999999999999996
133 Os.27659.1.S1_x_at 0.999799678546418 0.999999999999993
134 Os.23381.1.A1_at 0.998384810871295 0.999999999999866
135 Os.27759.1.S1_at 0.99999999999947 0.90316417946214
136 OsAffx.7934.1.S1_at 9.67506653877832e-15 5.65381650012578e-14
137 Os.54672.1.S1_at 3.92476327401578e-15 3.92476327401578e-15
138 Os.15471.1.S1_at 0.581698414440978 2.65615551406177e-09
139 Os.31778.2.S1_at 5.10838635074007e-07 1.3889612535351e-13
140 Os.17652.1.S1_s_at 0.0154511215885179 9.67506653877832e-15
141 OsAffx.11963.1.S1_at 0.397817809904805 2.53369790186473e-14
142 OsAffx.27299.1.S1_at 0.0138504710992339 0.999999930408472
143 Os.5197.2.S1_x_at 3.92476327401578e-15 8.0257899988438e-15
144 Os.54653.1.S1_at 3.92476327401578e-15 3.92476327401578e-15
145 Os.16558.1.S1_at 0.347050602369086 1.21414887761266e-12
146 Os.35154.1.S1_x_at 5.30953621332251e-15 8.41107462030933e-14
147 Os.54178.1.S1_at 4.92385029896428e-15 1.60860855994897e-10
148 Os.46710.2.S1_at 0.999999999043055 0.99999999999925
149 Os.54318.1.S1_at 3.27480058990236e-14 8.33183570817745e-15
150 OsAffx.13338.1.S1_at 4.39646307568141e-15 9.56945150584442e-10
151 Os.46869.1.A1_at 0.807337862876547 6.09057043796986e-13
152 Os.44475.1.S1_x_at 0.862924569208568 6.31242983607681e-10
153 Os.17997.1.S1_at 0.701108584708885 1.43404313022749e-08
154 Os.32964.1.S1_at 3.65376652789413e-06 0.999999999999989
155 Os.49294.1.S1_at 5.3538105508122e-08 0.99999999999993
156 Os.26171.1.S1_at 0.999999991279402 0.999999999981307
157 Os.50450.1.S1_at 0.999999999693809 0.999999999999994
158 OsAffx.19332.1.S1_at 7.44650475049233e-15 0.232989926829363
159 OsAffx.28727.1.S1_at 6.33502828108896e-12 1.30319196276126e-14
160 Os.16904.1.S1_at 0.999999999999996 0.999999999999996
161 Os.6825.1.S1_at 0.0087944119683183 0.227163492847201
162 OsAffx.3504.1.S1_at 0.714290155730357 0.0117917462590248
163 Os.4415.1.S1_at 3.93081720930364e-14 3.7158508920231e-12
164 Os.11834.1.S1_at 4.03102420786909e-05 0.99969748042776
165 Os.37255.1.A1_at 0.408959717155736 0.999992896581193
166 Os.7674.1.S1_at 0.999999999999626 0.999799678546418
167 Os.56048.1.S1_s_at 3.92476327401578e-15 4.39269420205013e-12
168 OsAffx.15785.1.S1_at 0.11807141577282 0.384924078726979
169 Os.27624.1.S1_at 4.04361222716952e-11 0.999999999999996
170 OsAffx.29866.1.S1_at 5.30953621332251e-15 0.792569387556402
171 OsAffx.3569.1.S1_x_at 0.0272204916784457 1.89445815950918e-07
172 Os.6318.1.S1_at 0.24943255693902 0.999999999999996
173 OsAffx.27557.1.S1_at 3.92476327401578e-15 4.89008147727872e-14
174 Os.1479.1.S1_at 0.11432028443542 1.59594850002947e-12
175 OsAffx.24515.1.S1_at 3.92476327401578e-15 2.50037606489293e-11
176 Os.51295.1.S1_at 0.999927259590046 0.155765058812464
177 Os.11255.1.S1_at 9.54670346713074e-13 5.11311585323595e-15
178 OsAffx.31756.4.S1_x_at 4.39646307568141e-15 2.02491863866523e-12
179 Os.49226.1.S1_at 0.999999999999994 1.18474072609428e-11
180 OsAffx.17724.1.S1_at 0.0141932467963315 0.730367476362221
181 OsAffx.3755.1.S1_at 0.999999999999993 0.999999394540815
182 Os.18664.1.S1_a_at 0.998995196883764 0.99999999763306
183 Os.33087.1.S1_at 8.09426644968574e-06 0.999999999999994
184 Os.54146.1.S1_at 3.92476327401578e-15 1.71103540371855e-10
185 Os.11312.1.S1_s_at 3.92476327401578e-15 0.999999999999896
186 OsAffx.4923.1.S1_at 0.000348222211294648 0.999998397264933
187 OsAffx.29954.1.S1_at 7.23234617567231e-12 1.16798228595587e-07
188 OsAffx.27508.10.S1_s_at 0.302229477672359 0.999999999999973
189 Os.64.1.S1_at 4.07673948865954e-14 0.999999999999994
190 OsAffx.30868.1.S1_at 3.92476327401578e-15 5.94753040972601e-08
191 Os.12986.1.S1_at 0.816392402760777 1.95813709440537e-14
192 Os.52151.1.S1_at 1.92959981469297e-06 4.541884742328e-12
193 OsAffx.31107.1.S1_at 0.999999999999958 0.727188594229806
194 Os.51491.1.S1_at 6.10611894103502e-05 0.999999999999995
195 Os.11144.1.S1_at 2.50749348108444e-09 0.999999999987352
196 Os.11308.1.S1_at 5.30953621332251e-15 0.837255056899589
197 Os.40000.1.S1_at 3.92476327401578e-15 6.65389147686702e-15
198 Os.11251.1.S1_at 1.88719325968143e-14 7.44650475049233e-15
199 Os.5510.1.S1_at 0.457982267642454 0.999999999999996
200 Os.18830.1.S1_at 0.101861459454507 0.999620037752728
HubStatus
1 Not Hub
2 Unique Hub to Stress
3 Housekeeping Hub
4 Not Hub
5 Housekeeping Hub
6 Housekeeping Hub
7 Not Hub
8 Housekeeping Hub
9 Unique Hub to Stress
10 Housekeeping Hub
11 Not Hub
12 Housekeeping Hub
13 Housekeeping Hub
14 Unique Hub to Stress
15 Housekeeping Hub
16 Not Hub
17 Housekeeping Hub
18 Not Hub
19 Unique Hub to Normal
20 Unique Hub to Normal
21 Housekeeping Hub
22 Housekeeping Hub
23 Housekeeping Hub
24 Unique Hub to Stress
25 Housekeeping Hub
26 Unique Hub to Stress
27 Unique Hub to Stress
28 Not Hub
29 Not Hub
30 Not Hub
31 Housekeeping Hub
32 Housekeeping Hub
33 Not Hub
34 Not Hub
35 Not Hub
36 Unique Hub to Stress
37 Housekeeping Hub
38 Not Hub
39 Housekeeping Hub
40 Not Hub
41 Unique Hub to Stress
42 Not Hub
43 Not Hub
44 Not Hub
45 Housekeeping Hub
46 Unique Hub to Normal
47 Housekeeping Hub
48 Housekeeping Hub
49 Not Hub
50 Not Hub
51 Not Hub
52 Unique Hub to Stress
53 Unique Hub to Stress
54 Housekeeping Hub
55 Not Hub
56 Not Hub
57 Not Hub
58 Not Hub
59 Housekeeping Hub
60 Unique Hub to Stress
61 Unique Hub to Normal
62 Not Hub
63 Not Hub
64 Not Hub
65 Housekeeping Hub
66 Unique Hub to Normal
67 Housekeeping Hub
68 Unique Hub to Stress
69 Not Hub
70 Unique Hub to Normal
71 Not Hub
72 Not Hub
73 Unique Hub to Normal
74 Unique Hub to Normal
75 Not Hub
76 Housekeeping Hub
77 Not Hub
78 Not Hub
79 Not Hub
80 Housekeeping Hub
81 Housekeeping Hub
82 Not Hub
83 Housekeeping Hub
84 Housekeeping Hub
85 Unique Hub to Normal
86 Housekeeping Hub
87 Not Hub
88 Unique Hub to Stress
89 Unique Hub to Normal
90 Not Hub
91 Housekeeping Hub
92 Not Hub
93 Not Hub
94 Not Hub
95 Housekeeping Hub
96 Not Hub
97 Not Hub
98 Not Hub
99 Not Hub
100 Housekeeping Hub
101 Unique Hub to Normal
102 Not Hub
103 Not Hub
104 Unique Hub to Stress
105 Housekeeping Hub
106 Unique Hub to Normal
107 Not Hub
108 Housekeeping Hub
109 Not Hub
110 Unique Hub to Normal
111 Housekeeping Hub
112 Housekeeping Hub
113 Housekeeping Hub
114 Not Hub
115 Housekeeping Hub
116 Not Hub
117 Not Hub
118 Housekeeping Hub
119 Not Hub
120 Not Hub
121 Unique Hub to Normal
122 Not Hub
123 Not Hub
124 Not Hub
125 Unique Hub to Normal
126 Housekeeping Hub
127 Not Hub
128 Not Hub
129 Housekeeping Hub
130 Housekeeping Hub
131 Housekeeping Hub
132 Unique Hub to Stress
133 Not Hub
134 Not Hub
135 Not Hub
136 Housekeeping Hub
137 Housekeeping Hub
138 Unique Hub to Normal
139 Housekeeping Hub
140 Unique Hub to Normal
141 Unique Hub to Normal
142 Not Hub
143 Housekeeping Hub
144 Housekeeping Hub
145 Unique Hub to Normal
146 Housekeeping Hub
147 Housekeeping Hub
148 Not Hub
149 Housekeeping Hub
150 Housekeeping Hub
151 Unique Hub to Normal
152 Unique Hub to Normal
153 Unique Hub to Normal
154 Unique Hub to Stress
155 Unique Hub to Stress
156 Not Hub
157 Not Hub
158 Unique Hub to Stress
159 Housekeeping Hub
160 Not Hub
161 Not Hub
162 Not Hub
163 Housekeeping Hub
164 Unique Hub to Stress
165 Not Hub
166 Not Hub
167 Housekeeping Hub
168 Not Hub
169 Unique Hub to Stress
170 Unique Hub to Stress
171 Unique Hub to Normal
172 Not Hub
173 Housekeeping Hub
174 Unique Hub to Normal
175 Housekeeping Hub
176 Not Hub
177 Housekeeping Hub
178 Housekeeping Hub
179 Unique Hub to Normal
180 Not Hub
181 Not Hub
182 Not Hub
183 Unique Hub to Stress
184 Housekeeping Hub
185 Unique Hub to Stress
186 Not Hub
187 Housekeeping Hub
188 Not Hub
189 Unique Hub to Stress
190 Housekeeping Hub
191 Unique Hub to Normal
192 Housekeeping Hub
193 Not Hub
194 Unique Hub to Stress
195 Unique Hub to Stress
196 Unique Hub to Stress
197 Housekeeping Hub
198 Housekeeping Hub
199 Not Hub
200 Not Hub
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