Description Usage Arguments Value Author(s) Examples
The function returns hub status of each gene in a gene co-expression network (GCN)
1 | HubStatus(pvalue.stress, pvalue.control, alpha)
|
pvalue.stress |
pvalue.stress is a vector of p-values for genes in the GCN under stress condition. pvalue.stress can be obtained from the output of hub.stress function. |
pvalue.control |
pvalue.control is a vector of p-values for genes in the GCN under normal or control condition. pvalue.control can be obtained from the output of hub.control function. |
alpha |
alpha is a scalar representing statistical level of significance. Default is alpha=0.0001 |
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
Samarendra Das and Baidya Nath Mandal
1 2 3 4 5 6 7 8 | data(rice_salt)
pval.stres <- pvalue.hub(rice_salt, beta=6, m=18, s=80, plot=FALSE)
p1 <- pval.stres[, 2]
data(rice_normal)
pval.control <- pvalue.hub(rice_normal, beta=6, m=18, s=80, plot=FALSE)
p2 <- pval.control[, 2]
HubStatus(p1,p2,alpha=0.0001)
|
Loading required package: VennDiagram
Loading required package: grid
Loading required package: futile.logger
$hub.status
Genes Hub Status
1 Os.9805.1.S1_at Not Hub
2 Os.8149.1.S1_at Not Hub
3 Os.51343.1.S1_at Housekeeping Hub
4 Os.2881.1.S1_at Not Hub
5 Os.55524.1.S1_at Housekeeping Hub
6 Os.22029.1.S1_a_at Housekeeping Hub
7 OsAffx.3191.1.A1_at Not Hub
8 OsAffx.12383.1.S1_at Housekeeping Hub
9 Os.52157.1.S1_x_at Unique Hub to Stress
10 Os.26770.2.S1_x_at Housekeeping Hub
11 Os.5140.1.S1_at Not Hub
12 Os.2128.1.S1_at Unique Hub to Normal
13 Os.25613.1.A1_at Housekeeping Hub
14 Os.32686.1.S1_at Not Hub
15 OsAffx.27459.3.S1_at Housekeeping Hub
16 Os.10487.1.S1_at Not Hub
17 Os.31191.1.S1_at Housekeeping Hub
18 Os.53177.1.S1_at Not Hub
19 Os.40338.1.S1_at Unique Hub to Normal
20 Os.31171.1.S1_at Unique Hub to Normal
21 OsAffx.25039.1.S1_at Housekeeping Hub
22 OsAffx.12783.1.S1_at Housekeeping Hub
23 Os.47413.1.S1_at Housekeeping Hub
24 Os.38638.4.S1_s_at Unique Hub to Stress
25 Os.4819.1.A1_s_at Housekeeping Hub
26 Os.33971.1.S1_at Unique Hub to Stress
27 Os.18955.1.S1_at Unique Hub to Stress
28 Os.30269.1.S1_at Not Hub
29 Os.38812.1.S1_at Not Hub
30 Os.49650.1.S1_at Not Hub
31 OsAffx.27459.3.S1_x_at Housekeeping Hub
32 OsAffx.28409.1.S1_at Housekeeping Hub
33 Os.11151.1.S1_a_at Not Hub
34 Os.26511.1.S1_at Not Hub
35 Os.41199.1.A1_at Not Hub
36 Os.40007.1.S1_x_at Unique Hub to Stress
37 Os.10389.1.S1_at Housekeeping Hub
38 OsAffx.20682.1.S1_at Unique Hub to Stress
39 Os.11272.1.S1_at Housekeeping Hub
40 Os.9445.1.S1_at Not Hub
41 Os.48215.1.A1_at Unique Hub to Stress
42 Os.8673.1.S1_at Not Hub
43 Os.1465.1.S1_at Not Hub
44 Os.53177.1.S1_s_at Not Hub
45 OsAffx.28409.2.S1_s_at Housekeeping Hub
46 Os.53439.1.S1_at Unique Hub to Normal
47 Os.12629.1.S1_at Housekeeping Hub
48 Os.11555.1.S1_at Housekeeping Hub
49 Os.11898.1.S1_at Not Hub
50 Os.56232.1.S1_at Unique Hub to Normal
51 OsAffx.20930.1.S1_at Not Hub
52 Os.47737.1.S1_at Unique Hub to Stress
53 OsAffx.17611.1.S1_at Unique Hub to Stress
54 Os.38638.3.S1_x_at Housekeeping Hub
55 Os.52100.1.S1_at Not Hub
56 Os.7770.1.S1_at Not Hub
57 Os.9836.1.S1_at Not Hub
58 Os.16744.1.S1_at Not Hub
59 Os.51307.1.S1_at Housekeeping Hub
60 OsAffx.26317.1.S2_at Unique Hub to Stress
61 OsAffx.2166.1.S1_at Unique Hub to Normal
62 Os.5621.1.S1_at Not Hub
63 Os.11787.1.S1_at Not Hub
64 Os.33625.4.S1_at Not Hub
65 OsAffx.31756.4.S1_at Housekeeping Hub
66 Os.50805.1.S1_at Unique Hub to Normal
67 OsAffx.29448.1.S1_at Housekeeping Hub
68 Os.11801.1.S1_at Unique Hub to Stress
69 Os.47802.1.A1_at Not Hub
70 OsAffx.18861.1.S1_at Unique Hub to Normal
71 Os.56150.1.S1_at Not Hub
72 Os.12642.1.S1_at Not Hub
73 Os.10469.1.S1_at Unique Hub to Normal
74 Os.55079.1.S1_at Unique Hub to Normal
75 Os.34174.1.S1_at Not Hub
76 OsAffx.12433.1.S1_at Housekeeping Hub
77 Os.50369.1.S1_at Not Hub
78 OsAffx.15447.1.S1_at Not Hub
79 Os.52619.1.S1_at Not Hub
80 Os.17102.1.S1_at Housekeeping Hub
81 OsAffx.30295.1.S1_at Housekeeping Hub
82 Os.11800.1.S1_s_at Not Hub
83 Os.10654.1.S1_s_at Housekeeping Hub
84 Os.54579.1.S1_s_at Housekeeping Hub
85 OsAffx.3569.1.S1_at Unique Hub to Normal
86 Os.55907.1.S1_at Housekeeping Hub
87 Os.52058.1.S1_at Not Hub
88 Os.57456.1.S1_x_at Unique Hub to Stress
89 Os.155.1.S1_a_at Unique Hub to Normal
90 Os.6345.1.S1_at Not Hub
91 Os.11677.1.S1_x_at Housekeeping Hub
92 OsAffx.8061.1.S1_at Not Hub
93 OsAffx.13662.1.S1_at Not Hub
94 Os.15199.1.S1_at Not Hub
95 Os.31778.2.S1_x_at Housekeeping Hub
96 Os.39994.1.S1_at Not Hub
97 Os.50372.1.S1_at Not Hub
98 Os.18381.1.S1_at Not Hub
99 Os.11796.1.S1_at Not Hub
100 OsAffx.19632.1.S1_at Housekeeping Hub
101 Os.12767.1.S1_a_at Unique Hub to Normal
102 Os.34061.1.S1_a_at Not Hub
103 Os.12239.1.S1_at Not Hub
104 Os.49780.1.S1_x_at Unique Hub to Stress
105 OsAffx.7332.1.S1_at Housekeeping Hub
106 Os.36162.1.S1_s_at Unique Hub to Normal
107 Os.44475.1.S1_at Not Hub
108 Os.54555.1.S1_at Housekeeping Hub
109 Os.15247.1.S1_s_at Not Hub
110 Os.6683.1.S1_at Unique Hub to Normal
111 Os.56924.1.S1_at Housekeeping Hub
112 OsAffx.15530.1.S1_at Housekeeping Hub
113 Os.50290.1.S1_at Housekeeping Hub
114 Os.57362.1.S1_at Not Hub
115 Os.50883.1.S1_at Housekeeping Hub
116 Os.12286.1.S1_at Not Hub
117 Os.52536.1.S1_at Not Hub
118 Os.6792.1.S1_at Housekeeping Hub
119 Os.319.1.A1_at Not Hub
120 Os.18933.1.S1_at Not Hub
121 Os.4760.1.S1_at Unique Hub to Normal
122 OsAffx.30721.5.S1_at Not Hub
123 OsAffx.15125.1.S1_at Not Hub
124 Os.26802.1.S1_at Not Hub
125 Os.11786.2.S1_at Unique Hub to Normal
126 Os.47413.1.S1_x_at Housekeeping Hub
127 Os.24906.1.S1_at Not Hub
128 Os.4715.1.S1_at Not Hub
129 Os.534.2.S1_x_at Housekeeping Hub
130 Os.8118.1.S1_at Housekeeping Hub
131 Os.21319.1.S1_at Unique Hub to Normal
132 Os.23183.1.S1_at Unique Hub to Stress
133 Os.27659.1.S1_x_at Not Hub
134 Os.23381.1.A1_at Not Hub
135 Os.27759.1.S1_at Not Hub
136 OsAffx.7934.1.S1_at Housekeeping Hub
137 Os.54672.1.S1_at Housekeeping Hub
138 Os.15471.1.S1_at Unique Hub to Normal
139 Os.31778.2.S1_at Housekeeping Hub
140 Os.17652.1.S1_s_at Unique Hub to Normal
141 OsAffx.11963.1.S1_at Unique Hub to Normal
142 OsAffx.27299.1.S1_at Not Hub
143 Os.5197.2.S1_x_at Housekeeping Hub
144 Os.54653.1.S1_at Housekeeping Hub
145 Os.16558.1.S1_at Unique Hub to Normal
146 Os.35154.1.S1_x_at Housekeeping Hub
147 Os.54178.1.S1_at Housekeeping Hub
148 Os.46710.2.S1_at Not Hub
149 Os.54318.1.S1_at Housekeeping Hub
150 OsAffx.13338.1.S1_at Housekeeping Hub
151 Os.46869.1.A1_at Unique Hub to Normal
152 Os.44475.1.S1_x_at Unique Hub to Normal
153 Os.17997.1.S1_at Unique Hub to Normal
154 Os.32964.1.S1_at Not Hub
155 Os.49294.1.S1_at Unique Hub to Stress
156 Os.26171.1.S1_at Not Hub
157 Os.50450.1.S1_at Not Hub
158 OsAffx.19332.1.S1_at Unique Hub to Stress
159 OsAffx.28727.1.S1_at Housekeeping Hub
160 Os.16904.1.S1_at Not Hub
161 Os.6825.1.S1_at Not Hub
162 OsAffx.3504.1.S1_at Not Hub
163 Os.4415.1.S1_at Housekeeping Hub
164 Os.11834.1.S1_at Not Hub
165 Os.37255.1.A1_at Not Hub
166 Os.7674.1.S1_at Not Hub
167 Os.56048.1.S1_s_at Housekeeping Hub
168 OsAffx.15785.1.S1_at Not Hub
169 Os.27624.1.S1_at Unique Hub to Stress
170 OsAffx.29866.1.S1_at Unique Hub to Stress
171 OsAffx.3569.1.S1_x_at Unique Hub to Normal
172 Os.6318.1.S1_at Not Hub
173 OsAffx.27557.1.S1_at Housekeeping Hub
174 Os.1479.1.S1_at Unique Hub to Normal
175 OsAffx.24515.1.S1_at Housekeeping Hub
176 Os.51295.1.S1_at Not Hub
177 Os.11255.1.S1_at Housekeeping Hub
178 OsAffx.31756.4.S1_x_at Housekeeping Hub
179 Os.49226.1.S1_at Unique Hub to Normal
180 OsAffx.17724.1.S1_at Not Hub
181 OsAffx.3755.1.S1_at Not Hub
182 Os.18664.1.S1_a_at Not Hub
183 Os.33087.1.S1_at Unique Hub to Stress
184 Os.54146.1.S1_at Housekeeping Hub
185 Os.11312.1.S1_s_at Unique Hub to Stress
186 OsAffx.4923.1.S1_at Not Hub
187 OsAffx.29954.1.S1_at Housekeeping Hub
188 OsAffx.27508.10.S1_s_at Not Hub
189 Os.64.1.S1_at Unique Hub to Stress
190 OsAffx.30868.1.S1_at Housekeeping Hub
191 Os.12986.1.S1_at Unique Hub to Normal
192 Os.52151.1.S1_at Unique Hub to Normal
193 OsAffx.31107.1.S1_at Not Hub
194 Os.51491.1.S1_at Not Hub
195 Os.11144.1.S1_at Unique Hub to Stress
196 Os.11308.1.S1_at Unique Hub to Stress
197 Os.40000.1.S1_at Housekeeping Hub
198 Os.11251.1.S1_at Housekeeping Hub
199 Os.5510.1.S1_at Not Hub
200 Os.18830.1.S1_at Not Hub
$out1
Housekeeping Hub Not Hub Unique Hub to Normal
63 84 30
Unique Hub to Stress
23
attr(,"class")
[1] "HubStatus_Genes" "HubStatus_Matrix"
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