Mercurial > repos > fubar > rglasso_1_9_8

comparison test-data/coxlassotest.html @ 0:b539dcdc6168 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Imported from capsule None
author fubar
date Sun, 19 Oct 2014 06:04:51 -0400
parents
children 4b62ea84c318
comparison
equal deleted inserted replaced
-1:000000000000 0:b539dcdc6168
1 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
2 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
3 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
4 <meta name="generator" content="Galaxy rgToolFactory.py tool output - see http://g2.trac.bx.psu.edu/" />
5 <title></title>
6 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
7 </head>
8 <body>
9 <div class="toolFormBody">
10
11 <div class="infomessage">Galaxy Tool "rglasso" run at 19/10/2014 13:11:14</div><br/>
12 <div class="toolFormTitle">cox images and outputs</div>
13 (Click on a thumbnail image to download the corresponding original PDF image)<br/>
14 <div><table class="simple" cellpadding="2" cellspacing="2">
15 <tr>
16 <td><a href="cox_Coxglmnettest_glmnet_cvdeviance.pdf"><img src="cox_Coxglmnettest_glmnet_cvdeviance.png" title="Click to download a PDF of cox_Coxglmnettest_glmnet_cvdeviance.pdf" hspace="5" width="400"
17 alt="Image called cox_Coxglmnettest_glmnet_cvdeviance.pdf"/></a></td>
18
19 <td><a href="cox_Coxglmnettest_glmnetdev.pdf"><img src="cox_Coxglmnettest_glmnetdev.png" title="Click to download a PDF of cox_Coxglmnettest_glmnetdev.pdf" hspace="5" width="400"
20 alt="Image called cox_Coxglmnettest_glmnetdev.pdf"/></a></td>
21 </tr>
22
23 </table></div>
24
25 <div class="toolFormTitle">cox log output</div>
26
27 <pre>
28
29 [1] "All partial likelihood coefficients from Cox model at minimum lambda of 0.00138091491730048:"
30
31 3 x 1 sparse Matrix of class "dgCMatrix"
32
33 1
34
35 rhubarb 1.124517e-03
36
37 vegemite 1.444990e-01
38
39 apple 3.344565e-06
40
41
42 </pre>
43
44 <div class="toolFormTitle">rglasso log output</div>
45
46 <pre>
47
48 Loading required package: Matrix
49
50 Loading required package: methods
51
52 Loaded glmnet 1.9-8
53
54 Loaded lars 1.2
55
56 Warning messages:
57
58 1: In if (class(larsres) == "try-error") { :
59
60 the condition has length > 1 and only the first element will be used
61
62 2: In plot.window(...) : "label" is not a graphical parameter
63
64 3: In plot.xy(xy, type, ...) : "label" is not a graphical parameter
65
66 4: In axis(side = side, at = at, labels = labels, ...) :
67
68 "label" is not a graphical parameter
69
70 5: In axis(side = side, at = at, labels = labels, ...) :
71
72 "label" is not a graphical parameter
73
74 6: In box(...) : "label" is not a graphical parameter
75
76 7: In title(...) : "label" is not a graphical parameter
77
78
79 </pre>
80
81 <div class="toolFormTitle">Other log output</div>
82
83 <pre>
84
85 ## Toolfactory generated command line = Rscript - None None
86
87 [1] Cox model: Got yvar= time,status cols 1 n preds= 3 forced in= 3
88
89 [2] Cox model: Got yvar= time,status cols 2 n preds= 3 forced in= 3
90
91 [1] Results preview:
92
93 regulator partial_likelihood forced_in glmnet_model best_lambda
94
95 rhubarb rhubarb 0.001180324 TRUE cox 0.01508333
96
97 vegemite vegemite 0.093827440 FALSE cox 0.01508333
98
99 [1] SessionInfo for this R session:
100
101 R version 3.1.0 (2014-04-10)
102
103 Platform: x86_64-unknown-linux-gnu (64-bit)
104
105 locale:
106
107 [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
108
109 [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 LC_PAPER=en_AU.UTF-8 LC_NAME=C
110
111 [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
112
113 attached base packages:
114
115 [1] methods stats graphics grDevices utils datasets base
116
117 other attached packages:
118
119 [1] lars_1.2 glmnet_1.9-8 Matrix_1.1-4
120
121 loaded via a namespace (and not attached):
122
123 [1] grid_3.1.0 lattice_0.20-29
124
125
126 </pre>
127
128 <div class="toolFormTitle">All output files available for downloading</div>
129
130 <div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>
131
132 <tr><td><a href="cox_Coxglmnettest_glmnet_cvdeviance.pdf">cox_Coxglmnettest_glmnet_cvdeviance.pdf</a></td><td>6.4 KB</td></tr>
133 <tr class="odd_row"><td><a href="cox_Coxglmnettest_glmnetdev.pdf">cox_Coxglmnettest_glmnetdev.pdf</a></td><td>5.2 KB</td></tr>
134 <tr><td><a href="cox_rglasso.log">cox_rglasso.log</a></td><td>228 B</td></tr>
135 <tr class="odd_row"><td><a href="rglasso.Rscript">rglasso.Rscript</a></td><td>9.8 KB</td></tr>
136 <tr><td><a href="rglasso_error.log">rglasso_error.log</a></td><td>671 B</td></tr>
137 <tr class="odd_row"><td><a href="rglasso_runner.log">rglasso_runner.log</a></td><td>1.1 KB</td></tr>
138 </table></div><br/>
139 </div></body></html>
140