-
Notifications
You must be signed in to change notification settings - Fork 0
/
pmcor.html
84 lines (59 loc) · 2.18 KB
/
pmcor.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html><head><title>R: Generate the SCNA Significance Plots of Two Types</title>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<link rel="stylesheet" type="text/css" href="R.css">
</head><body>
<table width="100%" summary="page for pmcor"><tr><td>pmcor</td><td align="right">R Documentation</td></tr></table>
<h2>Generate the SCNA Significance Plots of Two Types</h2>
<h3>Description</h3>
<p>Generate the SCNA significance plots of two types:
</p>
<p>whole-genome based:
</p>
<p>if a SCNA region spans exome boundaries, interpolate between the two
exomes (by showing CN level in the intron segment at the same level as
in the two flanking exons).
</p>
<p>coverage-based: i.e., plotting only the region covered by the
sequencing reads (in our case, the MCOR regions). This will be
achieved by constructing the x-axis as the joining of all the regions.
</p>
<p>For both, we discussed having different options on how to join
non-adjacent regions ('zero', 'interpolation', 'min').
</p>
<h3>Usage</h3>
<pre>
pmcor(file, base.on="coverage", join.method)
</pre>
<h3>Arguments</h3>
<table summary="R argblock">
<tr valign="top"><td><code>file</code></td>
<td>
<p>file is the location of the file containing the mcor
output their genomic coordiantes.</p>
</td></tr>
<tr valign="top"><td><code>base.on</code></td>
<td>
<p>base.on should be "coverage" or "genome"</p>
</td></tr>
<tr valign="top"><td><code>join.method</code></td>
<td>
<p>join.method should be "zero", "interpolate" or "min"</p>
</td></tr>
</table>
<h3>Author(s)</h3>
<p>Yu Fu <a href="mailto:[email protected]">[email protected]</a></p>
<h3>References</h3>
<p><a href="https://projects.zoho.com/portal/montilab#wiki/465555000000032025/Scoring-SCNAs.html">https://projects.zoho.com/portal/montilab#wiki/465555000000032025/Scoring-SCNAs.html</a>
</p>
<h3>See Also</h3>
<p><code>pmatch</code>, <code>ggplot</code>
</p>
<h3>Examples</h3>
<pre>
## Using the default parameters
pmcor(file, base.on="coverage", join.method)
## Using other "bases" and joining method
pmcor(file, base.on="coverage", joining.method="min")
</pre>
</body></html>