listPathwayComponents: This function lists all pathway components of a given...
In rBiopaxParser: Parses BioPax files and represents them in R
Description
Usage
Arguments
Value
Author(s)
Examples
Description
This function returns a (unique) data.frame listing all component IDs, names and classes of the supplied pathway.
Usage
1
2
3
4
5
6
7
listPathwayComponents(
biopax,
id,
includeSubPathways = TRUE,
returnIDonly = FALSE,
biopaxlevel = 3
)
Arguments
biopax
A biopax model
id
string. A pathway ID
includeSubPathways
logical. If TRUE the returned list will include subpathways and pathwaysteps as well.
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
data.frame
Author(s)
Frank Kramer
Examples
1
2
3
# load data
data(biopaxexample)
listPathwayComponents(biopax, id="pid_p_100002_wntpathway")
Example output
Loading required package: data.table
id name
1 ex_i_100039 protein ubiquitination
2 ex_i_100040 degradation
3 ex_i_100046_2
4 ex_i_100046_2
5 ex_i_100046_2
6 ex_i_100046_2_activator_1
7 ex_i_100046_2_activator_1
8 ex_i_100046_2_activator_1
9 ex_i_100046_2_inhibitor_1
10 ex_i_100046_2_inhibitor_1
11 ex_i_100046_2_inhibitor_1
12 ex_i_100052
13 ex_i_100052
14 ex_i_100052
15 ex_i_100052
16 ex_i_100052
17 ex_i_100036
18 ex_i_100036
19 ex_i_100036
20 ex_i_100036
21 ex_i_100036
22 ex_i_100036
23 ex_i_100036_activator_1
24 ex_i_100036_activator_1
25 ex_i_100036_activator_1
26 ex_i_100036_inhibitor_1
27 ex_i_100036_inhibitor_1
28 ex_i_100036_inhibitor_1
29 ex_i_100050
30 ex_i_100050
31 ex_i_100050
32 ex_i_100050
33 ex_i_100050
34 ex_i_100050
35 ex_i_100043
36 ex_i_100043
37 ex_i_100043
38 ex_i_100043
39 ex_i_100043_activator_1
40 ex_i_100043_activator_1
41 ex_i_100043_activator_1
42 ex_i_100038
43 ex_i_100038
44 ex_i_100038
45 ex_i_100038
46 ex_i_100038
47 ex_i_100053
48 ex_i_100053
49 ex_i_100053
50 ex_i_100053
51 ex_i_100053
52 ex_i_100053_inhibitor_1
53 ex_i_100053_inhibitor_1
54 ex_i_100053_inhibitor_1
55 ex_i_100045
56 ex_i_100045
57 ex_i_100045
58 ex_i_100045
59 ex_i_100045_activator_1
60 ex_i_100045_activator_1
61 ex_i_100045_activator_1
62 ex_i_100034
63 ex_i_100034
64 ex_i_100034
65 ex_i_100034
66 ex_i_100034_activator_1
67 ex_i_100034_activator_1
68 ex_i_100034_activator_1
69 ex_i_100042
70 ex_i_100042
71 ex_i_100042
72 ex_i_100042
73 ex_i_100042_activator_1
74 ex_i_100042_activator_1
75 ex_i_100042_activator_1
76 ex_i_100049
77 ex_i_100049
78 ex_i_100049
79 ex_i_100049
80 ex_i_100049_activator_1
81 ex_i_100049_activator_1
82 ex_i_100049_activator_1
83 ex_i_100049_activator_2
84 ex_i_100049_activator_2
85 ex_i_100049_activator_2
86 ex_i_100049_inhibitor_1
87 ex_i_100049_inhibitor_1
88 ex_i_100049_inhibitor_1
89 ex_i_100037
90 ex_i_100037
91 ex_i_100037
92 ex_i_100037
93 ex_i_100037
94 ex_i_100037
95 ex_i_100037_activator_1
96 ex_i_100037_activator_1
97 ex_i_100037_activator_1
98 ex_i_100037_inhibitor_1
99 ex_i_100037_inhibitor_1
100 ex_i_100037_inhibitor_1
101 ex_i_100044
102 ex_i_100044
103 ex_i_100044
104 ex_i_100044
105 ex_i_100044
106 ex_i_100044_inhibitor_1
107 ex_i_100044_inhibitor_1
108 ex_i_100044_inhibitor_1
109 ex_i_100041
110 ex_i_100041
111 ex_i_100041
112 ex_i_100041
113 ex_i_100046_3
114 ex_i_100046_3
115 ex_i_100046_3
116 ex_i_100046_3_activator_1
117 ex_i_100046_3_activator_1
118 ex_i_100046_3_activator_1
119 ex_i_100046_3_inhibitor_1
120 ex_i_100046_3_inhibitor_1
121 ex_i_100046_3_inhibitor_1
122 ex_i_100048
123 ex_i_100048
124 ex_i_100048
125 ex_i_100048
126 ex_i_100048_activator_1
127 ex_i_100048_activator_1
128 ex_i_100048_activator_1
129 ex_i_100048_activator_2
130 ex_i_100048_activator_2
131 ex_i_100048_activator_2
132 ex_i_100048_inhibitor_1
133 ex_i_100048_inhibitor_1
134 ex_i_100048_inhibitor_1
135 ex_i_100046_1
136 ex_i_100046_1
137 ex_i_100046_1
138 ex_i_100046_1_activator_1
139 ex_i_100046_1_activator_1
140 ex_i_100046_1_activator_1
141 ex_i_100046_1_inhibitor_1
142 ex_i_100046_1_inhibitor_1
143 ex_i_100046_1_inhibitor_1
144 ex_i_100035
145 ex_i_100035
146 ex_i_100035
147 ex_i_100035
148 ex_i_100035
149 ex_i_100035
150 ex_i_100035
151 ex_i_100035
152 ex_i_100035_activator_1
153 ex_i_100035_activator_1
154 ex_i_100035_activator_1
155 ex_i_100051
156 ex_i_100051
157 ex_i_100051
158 ex_i_100051
159 ex_i_100051
160 ex_i_100051
161 ex_i_100047
162 ex_i_100047
163 ex_i_100047
164 ex_i_100047
165 ex_i_100047
166 ex_i_100047
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 returns a (unique) data.frame listing all component IDs, names and classes of the supplied pathway.
Usage
1 2 3 4 5 6 7 | listPathwayComponents(
biopax,
id,
includeSubPathways = TRUE,
returnIDonly = FALSE,
biopaxlevel = 3
)
|
Arguments
biopax |
A biopax model |
id |
string. A pathway ID |
includeSubPathways |
logical. If TRUE the returned list will include subpathways and pathwaysteps as well. |
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
data.frame
Author(s)
Frank Kramer
Examples
1 2 3 | # load data
data(biopaxexample)
listPathwayComponents(biopax, id="pid_p_100002_wntpathway")
|
Example output
Loading required package: data.table
id name
1 ex_i_100039 protein ubiquitination
2 ex_i_100040 degradation
3 ex_i_100046_2
4 ex_i_100046_2
5 ex_i_100046_2
6 ex_i_100046_2_activator_1
7 ex_i_100046_2_activator_1
8 ex_i_100046_2_activator_1
9 ex_i_100046_2_inhibitor_1
10 ex_i_100046_2_inhibitor_1
11 ex_i_100046_2_inhibitor_1
12 ex_i_100052
13 ex_i_100052
14 ex_i_100052
15 ex_i_100052
16 ex_i_100052
17 ex_i_100036
18 ex_i_100036
19 ex_i_100036
20 ex_i_100036
21 ex_i_100036
22 ex_i_100036
23 ex_i_100036_activator_1
24 ex_i_100036_activator_1
25 ex_i_100036_activator_1
26 ex_i_100036_inhibitor_1
27 ex_i_100036_inhibitor_1
28 ex_i_100036_inhibitor_1
29 ex_i_100050
30 ex_i_100050
31 ex_i_100050
32 ex_i_100050
33 ex_i_100050
34 ex_i_100050
35 ex_i_100043
36 ex_i_100043
37 ex_i_100043
38 ex_i_100043
39 ex_i_100043_activator_1
40 ex_i_100043_activator_1
41 ex_i_100043_activator_1
42 ex_i_100038
43 ex_i_100038
44 ex_i_100038
45 ex_i_100038
46 ex_i_100038
47 ex_i_100053
48 ex_i_100053
49 ex_i_100053
50 ex_i_100053
51 ex_i_100053
52 ex_i_100053_inhibitor_1
53 ex_i_100053_inhibitor_1
54 ex_i_100053_inhibitor_1
55 ex_i_100045
56 ex_i_100045
57 ex_i_100045
58 ex_i_100045
59 ex_i_100045_activator_1
60 ex_i_100045_activator_1
61 ex_i_100045_activator_1
62 ex_i_100034
63 ex_i_100034
64 ex_i_100034
65 ex_i_100034
66 ex_i_100034_activator_1
67 ex_i_100034_activator_1
68 ex_i_100034_activator_1
69 ex_i_100042
70 ex_i_100042
71 ex_i_100042
72 ex_i_100042
73 ex_i_100042_activator_1
74 ex_i_100042_activator_1
75 ex_i_100042_activator_1
76 ex_i_100049
77 ex_i_100049
78 ex_i_100049
79 ex_i_100049
80 ex_i_100049_activator_1
81 ex_i_100049_activator_1
82 ex_i_100049_activator_1
83 ex_i_100049_activator_2
84 ex_i_100049_activator_2
85 ex_i_100049_activator_2
86 ex_i_100049_inhibitor_1
87 ex_i_100049_inhibitor_1
88 ex_i_100049_inhibitor_1
89 ex_i_100037
90 ex_i_100037
91 ex_i_100037
92 ex_i_100037
93 ex_i_100037
94 ex_i_100037
95 ex_i_100037_activator_1
96 ex_i_100037_activator_1
97 ex_i_100037_activator_1
98 ex_i_100037_inhibitor_1
99 ex_i_100037_inhibitor_1
100 ex_i_100037_inhibitor_1
101 ex_i_100044
102 ex_i_100044
103 ex_i_100044
104 ex_i_100044
105 ex_i_100044
106 ex_i_100044_inhibitor_1
107 ex_i_100044_inhibitor_1
108 ex_i_100044_inhibitor_1
109 ex_i_100041
110 ex_i_100041
111 ex_i_100041
112 ex_i_100041
113 ex_i_100046_3
114 ex_i_100046_3
115 ex_i_100046_3
116 ex_i_100046_3_activator_1
117 ex_i_100046_3_activator_1
118 ex_i_100046_3_activator_1
119 ex_i_100046_3_inhibitor_1
120 ex_i_100046_3_inhibitor_1
121 ex_i_100046_3_inhibitor_1
122 ex_i_100048
123 ex_i_100048
124 ex_i_100048
125 ex_i_100048
126 ex_i_100048_activator_1
127 ex_i_100048_activator_1
128 ex_i_100048_activator_1
129 ex_i_100048_activator_2
130 ex_i_100048_activator_2
131 ex_i_100048_activator_2
132 ex_i_100048_inhibitor_1
133 ex_i_100048_inhibitor_1
134 ex_i_100048_inhibitor_1
135 ex_i_100046_1
136 ex_i_100046_1
137 ex_i_100046_1
138 ex_i_100046_1_activator_1
139 ex_i_100046_1_activator_1
140 ex_i_100046_1_activator_1
141 ex_i_100046_1_inhibitor_1
142 ex_i_100046_1_inhibitor_1
143 ex_i_100046_1_inhibitor_1
144 ex_i_100035
145 ex_i_100035
146 ex_i_100035
147 ex_i_100035
148 ex_i_100035
149 ex_i_100035
150 ex_i_100035
151 ex_i_100035
152 ex_i_100035_activator_1
153 ex_i_100035_activator_1
154 ex_i_100035_activator_1
155 ex_i_100051
156 ex_i_100051
157 ex_i_100051
158 ex_i_100051
159 ex_i_100051
160 ex_i_100051
161 ex_i_100047
162 ex_i_100047
163 ex_i_100047
164 ex_i_100047
165 ex_i_100047
166 ex_i_100047
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