unknottedGroups: Partition basepairs into unknotted groups
In R4RNA: An R package for RNA visualization and analysis

Description Usage Arguments Value Author(s) See Also Examples

Breaks down input helices into basepairs, and assigns each basepair to a numbered group such that basepairs in each group are non-pseudoknotted relative to all other basepairs within the same group.

The algorithm is greedy and thus will not find the best combination of basepairs to minimize the number of groups.

1	unknottedGroups(helix)

helix

A helix data.frame.

An array of integers dictating the groups of each helix. Will only correspond to the input helix structure if the input had helices of length 1 (e.g. output of expandHelix).

Daniel Lai

colourByUnknottedGroups

expandHelix

1
2
3

    data(helix)
    known$group <- unknottedGroups(known)
    print(known)

Loading required package: Biostrings
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     i   j length value group
1    1  72      1    NA     1
2    2  71      1    NA     1
3    3  70      1    NA     1
4    4  69      1    NA     1
5    5  68      1    NA     1
6    6  67      1    NA     1
7    7  66      1    NA     1
8    8  65      1    NA     1
9    9  64      1    NA     1
10  16  59      1    NA     1
11  17  58      1    NA     1
12  18  57      1    NA     1
13  19  56      1    NA     1
14  20  55      1    NA     1
15  21  54      1    NA     1
16  22  53      1    NA     1
17  23  52      1    NA     1
18  24  51      1    NA     1
19  37 150      1    NA     2
20  38 149      1    NA     2
21  39 148      1    NA     2
22  40 147      1    NA     2
23  41 146      1    NA     2
24  42 145      1    NA     2
25  43 143      1    NA     2
26  77 113      1    NA     1
27  78 112      1    NA     1
28  79 111      1    NA     1
29  80 110      1    NA     1
30  83  94      1    NA     1
31  84  93      1    NA     1
32  85  92      1    NA     1
33  86  91      1    NA     1
34 100 141      1    NA     2
35 101 140      1    NA     2
36 102 139      1    NA     2
37 103 138      1    NA     2
38 105 136      1    NA     2
39 106 135      1    NA     2
40 107 134      1    NA     2
41 108 133      1    NA     2
42 109 132      1    NA     2
43 114 128      1    NA     1
44 116 126      1    NA     1
45 117 125      1    NA     1
46 118 124      1    NA     1
47 154 182      1    NA     1
48 155 181      1    NA     1
49 156 180      1    NA     1
50 157 179      1    NA     1
51 158 178      1    NA     1
52 162 175      1    NA     1
53 163 174      1    NA     1
54 164 173      1    NA     1
55 165 172      1    NA     1
56 167 198      1    NA     2
57 168 197      1    NA     2
58 169 196      1    NA     2
59 170 195      1    NA     2
60 171 194      1    NA     2