ct2coord: Generate coordinate file

In RRNA: Secondary Structure Plotting for RNA

Description

Creates a coordinate file from a CT file that has been loaded into a data frame

Usage

ct2coord(input)

Arguments

input

Data frame representing a ct file. Created from makeCt or loadCt

Value

Returns a coordinate file for the secondary structure represented in the CT file

Note

Pseudoknots sometimes cause trouble

Author(s)

JP Bida

See Also

RNAPlot

Examples

ct=makeCt("((((...(((((((....)))))))...((((...))))...))))",
          "CCCCAAAGGGGGGGAUUACCCCUCCUUUAAAAGGGUUUUCCCCCCC"
         )
coord=ct2coord(ct)
RNAPlot(coord)

Example output

    pos before after seq pos2 bound
2    47     46    48   A   47     0
210  48     47    49   A   48    -1
1     1      0     2   C    1    46
211   2      1     3   C    2    45
3     3      2     4   C    3    44
4     4      3     5   C    4    43
5     5      4     6   A    5     0
6     6      5     7   A    6     0
7     7      6     8   A    7     0
8     8      7     9   G    8    25
9     9      8    10   G    9    24
10   10      9    11   G   10    23
11   11     10    12   G   11    22
12   12     11    13   G   12    21
13   13     12    14   G   13    20
14   14     13    15   G   14    19
15   15     14    16   A   15     0
16   16     15    17   U   16     0
17   17     16    18   U   17     0
18   18     17    19   A   18     0
19   19     18    20   C   19    14
20   20     19    21   C   20    13
21   21     20    22   C   21    12
22   22     21    23   C   22    11
23   23     22    24   U   23    10
24   24     23    25   C   24     9
25   25     24    26   C   25     8
26   26     25    27   U   26     0
27   27     26    28   U   27     0
28   28     27    29   U   28     0
29   29     28    30   A   29    39
30   30     29    31   A   30    38
31   31     30    32   A   31    37
32   32     31    33   A   32    36
33   33     32    34   G   33     0
34   34     33    35   G   34     0
35   35     34    36   G   35     0
36   36     35    37   U   36    32
37   37     36    38   U   37    31
38   38     37    39   U   38    30
39   39     38    40   U   39    29
40   40     39    41   C   40     0
41   41     40    42   C   41     0
42   42     41    43   C   42     0
43   43     42    44   C   43     4
44   44     43    45   C   44     3
45   45     44    46   C   45     2
46   46     45    47   C   46     1
49    0     -1     1   A    0    47
50   -1     -2     0   A   -1    48
[1] "-1 48 0 0 0 1 -1 0"
$x
[1] -1

$y
[1] 0

[1] 1.047198
[1] "47 48 47"
[1] "46 47 46"
[1] "45 46 45"
[1] "44 45 44"
[1] "43 44 43"
[1] "New LOOPS:  c(4, 43)"
[1] 4
[1] "8 25 8.09545988021662 -1.78716459510875 8.96148528400106 -1.28716459510875 7.10093798484835 -1.89169305837641"
$x
[1] -0.9945219

$y
[1] -0.1045285

[1] 1.365999
[1] "24 25 24"
[1] "23 24 23"
[1] "22 23 22"
[1] "21 22 21"
[1] "20 21 20"
[1] "19 20 19"
[1] "29 39 8.96148528400106 2.28716459510875 8.09545988021662 2.78716459510875 9.54927053629353 1.47814760073381"
$x
[1] 0.5877853

$y
[1] -0.809017

[1] 1.365999
[1] "38 39 38"
[1] "37 38 37"
[1] "36 37 36"
[1] "New LOOPS:  c(14, 19)" "New LOOPS:  c(32, 36)"
[1] 14
[1] 32
[1] "default ranges used"
[1] "no sequences to match"

RRNA documentation built on May 2, 2019, 1:06 p.m.