pathway2Geneset: This function generates the gene set of a pathway. This...
In rBiopaxParser: Parses BioPax files and represents them in R
Description
Usage
Arguments
Value
Author(s)
Examples
Description
This function generates the gene set of a pathway.
This function generates a gene set of all physicalEntity's of a pathway. First all interactions of the pathway are retrieved and all components of these interactions are then listed.
Usage
1
pathway2Geneset(biopax, pwid, returnIDonly = FALSE, biopaxlevel = 3)
Arguments
biopax
A biopax model
pwid
string
returnIDonly
logical. If TRUE only IDs of the components are returned. This saves tiem for looking up names for every single ID.
biopaxlevel
integer. Set the biopax level here if you supply a data.table directly.
Value
Returns the gene set of the supplied pathway. Returns NULL if the pathway has no components.
Author(s)
Frank Kramer
Examples
1
2
3
4
# load data
data(biopaxexample)
pwid1 = "pid_p_100002_wntpathway"
pathway2Geneset(biopax, pwid=pwid1)
Example output
Loading required package: data.table
id name
1 ex_m_100647 P10
2 ex_m_100637 P11
3 ex_m_25631 P12
4 ex_m_100222 P13
5 ex_m_100645 P14
6 ex_m_100059 P15
7 ex_m_100643 P16
8 ex_m_100440 P17
9 ex_m_100652 P18
10 ex_m_100653 P_21/P_20/P_19
11 ex_m_100656 P19
12 ex_m_100655 P20
13 ex_m_100654 P21
14 ex_m_100659 P_23/P_20/P_22
15 ex_m_100657 P22
16 ex_m_100300 P23
17 ex_m_100658 P_24/P_20/P_22
18 ex_m_100299 P24
19 ex_m_100648 P25
20 ex_m_28131 P26
21 ex_m_100369 P27
22 ex_m_100638 P_28/P_26/P_11
23 ex_m_100636 P28
24 ex_m_100660 P_20/P_19
25 ex_m_100634 P29
26 ex_m_100644 P30
27 ex_m_100104 P31
28 ex_m_100651 P32
29 ex_m_100649 P33
30 ex_m_100640 P34
31 ex_m_100661 P35
32 ex_m_100635 P36
33 ex_m_100650 P_11/P_25/P_10/P_12/P_33/P_13
34 ex_m_100639 P37
35 ex_m_100641 P_11/P_34
36 ex_m_100301 P38
37 ex_m_26501 P39
38 ex_m_100646 P_10/P_12/P_25/P_33
39 ex_m_26515 P40
40 ex_m_100642 P_11/P_16
41 ex_i_100046_2
42 ex_i_100046_2
43 ex_i_100046_2
44 ex_i_100036
45 ex_i_100036
46 ex_i_100036
47 ex_i_100036
48 ex_i_100036
49 ex_i_100036
50 ex_i_100043
51 ex_i_100043
52 ex_i_100043
53 ex_i_100043
54 ex_i_100053
55 ex_i_100053
56 ex_i_100053
57 ex_i_100053
58 ex_i_100053
59 ex_i_100045
60 ex_i_100045
61 ex_i_100045
62 ex_i_100045
63 ex_i_100034
64 ex_i_100034
65 ex_i_100034
66 ex_i_100034
67 ex_i_100042
68 ex_i_100042
69 ex_i_100042
70 ex_i_100042
71 ex_i_100049
72 ex_i_100049
73 ex_i_100049
74 ex_i_100049
75 ex_i_100037
76 ex_i_100037
77 ex_i_100037
78 ex_i_100037
79 ex_i_100037
80 ex_i_100037
81 ex_i_100044
82 ex_i_100044
83 ex_i_100044
84 ex_i_100044
85 ex_i_100044
86 ex_i_100046_3
87 ex_i_100046_3
88 ex_i_100046_3
89 ex_i_100048
90 ex_i_100048
91 ex_i_100048
92 ex_i_100048
93 ex_i_100046_1
94 ex_i_100046_1
95 ex_i_100046_1
96 ex_i_100035
97 ex_i_100035
98 ex_i_100035
99 ex_i_100035
100 ex_i_100035
101 ex_i_100035
102 ex_i_100035
103 ex_i_100035
104 ex_x_100637
105 ex_x_100656_30
106 ex_x_100656_30
107 ex_x_100440
108 ex_x_100646_5569
109 ex_x_100646_5569
110 ex_x_100658_30
111 ex_x_100658_30
112 ex_x_100300_30
113 ex_x_100300_30
114 ex_x_100059
115 ex_x_100637_5907
116 ex_x_100637_5907
117 ex_x_25631
118 ex_x_100300
119 ex_x_100654_5830
120 ex_x_100654_5830
121 ex_x_100645
122 ex_x_100644_26
123 ex_x_100644_26
124 ex_x_100660_30
125 ex_x_100660_30
126 ex_x_100655_30
127 ex_x_100655_30
128 ex_x_100657
129 ex_x_100647
130 ex_x_100638_5907
131 ex_x_100638_5907
132 ex_x_100640
133 ex_x_100653
134 ex_x_100657_30
135 ex_x_100657_30
136 ex_x_100634_26
137 ex_x_100634_26
138 ex_x_100301
139 ex_x_100646_26_5569
140 ex_x_100646_26_5569
141 ex_x_100646_26_5569
142 ex_x_100650_5569
143 ex_x_100650_5569
144 ex_x_100634
145 ex_x_100369
146 ex_x_100652
147 ex_x_100656
148 ex_x_26501
149 ex_x_26515_26
150 ex_x_26515_26
151 ex_x_100635
152 ex_x_100636_26
153 ex_x_100636_26
154 ex_x_100639
155 ex_x_100222
156 ex_x_100641
157 ex_x_100637_5569
158 ex_x_100637_5569
159 ex_x_100661_5830
160 ex_x_100661_5830
161 ex_x_100637_26
162 ex_x_100637_26
163 ex_x_100299
164 ex_x_100643
165 ex_x_100659_30
166 ex_x_100659_30
167 ex_x_28131
168 ex_x_100636
169 ex_x_100104
170 ex_x_28131_26
171 ex_x_28131_26
172 ex_x_100651
173 ex_x_100655
174 ex_x_100299_30
175 ex_x_100299_30
176 ex_x_100649
177 ex_x_100642
178 ex_x_100635_26
179 ex_x_100635_26
180 ex_x_100644
181 ex_x_100648
rBiopaxParser documentation built on Nov. 8, 2020, 8:21 p.m.
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Description Usage Arguments Value Author(s) Examples
Description
This function generates the gene set of a pathway.
This function generates a gene set of all physicalEntity's of a pathway. First all interactions of the pathway are retrieved and all components of these interactions are then listed.
Usage
1 | pathway2Geneset(biopax, pwid, returnIDonly = FALSE, biopaxlevel = 3)
|
Arguments
biopax |
A biopax model |
pwid |
string |
returnIDonly |
logical. If TRUE only IDs of the components are returned. This saves tiem for looking up names for every single ID. |
biopaxlevel |
integer. Set the biopax level here if you supply a data.table directly. |
Value
Returns the gene set of the supplied pathway. Returns NULL if the pathway has no components.
Author(s)
Frank Kramer
Examples
1 2 3 4 | # load data
data(biopaxexample)
pwid1 = "pid_p_100002_wntpathway"
pathway2Geneset(biopax, pwid=pwid1)
|
Example output
Loading required package: data.table
id name
1 ex_m_100647 P10
2 ex_m_100637 P11
3 ex_m_25631 P12
4 ex_m_100222 P13
5 ex_m_100645 P14
6 ex_m_100059 P15
7 ex_m_100643 P16
8 ex_m_100440 P17
9 ex_m_100652 P18
10 ex_m_100653 P_21/P_20/P_19
11 ex_m_100656 P19
12 ex_m_100655 P20
13 ex_m_100654 P21
14 ex_m_100659 P_23/P_20/P_22
15 ex_m_100657 P22
16 ex_m_100300 P23
17 ex_m_100658 P_24/P_20/P_22
18 ex_m_100299 P24
19 ex_m_100648 P25
20 ex_m_28131 P26
21 ex_m_100369 P27
22 ex_m_100638 P_28/P_26/P_11
23 ex_m_100636 P28
24 ex_m_100660 P_20/P_19
25 ex_m_100634 P29
26 ex_m_100644 P30
27 ex_m_100104 P31
28 ex_m_100651 P32
29 ex_m_100649 P33
30 ex_m_100640 P34
31 ex_m_100661 P35
32 ex_m_100635 P36
33 ex_m_100650 P_11/P_25/P_10/P_12/P_33/P_13
34 ex_m_100639 P37
35 ex_m_100641 P_11/P_34
36 ex_m_100301 P38
37 ex_m_26501 P39
38 ex_m_100646 P_10/P_12/P_25/P_33
39 ex_m_26515 P40
40 ex_m_100642 P_11/P_16
41 ex_i_100046_2
42 ex_i_100046_2
43 ex_i_100046_2
44 ex_i_100036
45 ex_i_100036
46 ex_i_100036
47 ex_i_100036
48 ex_i_100036
49 ex_i_100036
50 ex_i_100043
51 ex_i_100043
52 ex_i_100043
53 ex_i_100043
54 ex_i_100053
55 ex_i_100053
56 ex_i_100053
57 ex_i_100053
58 ex_i_100053
59 ex_i_100045
60 ex_i_100045
61 ex_i_100045
62 ex_i_100045
63 ex_i_100034
64 ex_i_100034
65 ex_i_100034
66 ex_i_100034
67 ex_i_100042
68 ex_i_100042
69 ex_i_100042
70 ex_i_100042
71 ex_i_100049
72 ex_i_100049
73 ex_i_100049
74 ex_i_100049
75 ex_i_100037
76 ex_i_100037
77 ex_i_100037
78 ex_i_100037
79 ex_i_100037
80 ex_i_100037
81 ex_i_100044
82 ex_i_100044
83 ex_i_100044
84 ex_i_100044
85 ex_i_100044
86 ex_i_100046_3
87 ex_i_100046_3
88 ex_i_100046_3
89 ex_i_100048
90 ex_i_100048
91 ex_i_100048
92 ex_i_100048
93 ex_i_100046_1
94 ex_i_100046_1
95 ex_i_100046_1
96 ex_i_100035
97 ex_i_100035
98 ex_i_100035
99 ex_i_100035
100 ex_i_100035
101 ex_i_100035
102 ex_i_100035
103 ex_i_100035
104 ex_x_100637
105 ex_x_100656_30
106 ex_x_100656_30
107 ex_x_100440
108 ex_x_100646_5569
109 ex_x_100646_5569
110 ex_x_100658_30
111 ex_x_100658_30
112 ex_x_100300_30
113 ex_x_100300_30
114 ex_x_100059
115 ex_x_100637_5907
116 ex_x_100637_5907
117 ex_x_25631
118 ex_x_100300
119 ex_x_100654_5830
120 ex_x_100654_5830
121 ex_x_100645
122 ex_x_100644_26
123 ex_x_100644_26
124 ex_x_100660_30
125 ex_x_100660_30
126 ex_x_100655_30
127 ex_x_100655_30
128 ex_x_100657
129 ex_x_100647
130 ex_x_100638_5907
131 ex_x_100638_5907
132 ex_x_100640
133 ex_x_100653
134 ex_x_100657_30
135 ex_x_100657_30
136 ex_x_100634_26
137 ex_x_100634_26
138 ex_x_100301
139 ex_x_100646_26_5569
140 ex_x_100646_26_5569
141 ex_x_100646_26_5569
142 ex_x_100650_5569
143 ex_x_100650_5569
144 ex_x_100634
145 ex_x_100369
146 ex_x_100652
147 ex_x_100656
148 ex_x_26501
149 ex_x_26515_26
150 ex_x_26515_26
151 ex_x_100635
152 ex_x_100636_26
153 ex_x_100636_26
154 ex_x_100639
155 ex_x_100222
156 ex_x_100641
157 ex_x_100637_5569
158 ex_x_100637_5569
159 ex_x_100661_5830
160 ex_x_100661_5830
161 ex_x_100637_26
162 ex_x_100637_26
163 ex_x_100299
164 ex_x_100643
165 ex_x_100659_30
166 ex_x_100659_30
167 ex_x_28131
168 ex_x_100636
169 ex_x_100104
170 ex_x_28131_26
171 ex_x_28131_26
172 ex_x_100651
173 ex_x_100655
174 ex_x_100299_30
175 ex_x_100299_30
176 ex_x_100649
177 ex_x_100642
178 ex_x_100635_26
179 ex_x_100635_26
180 ex_x_100644
181 ex_x_100648
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