Galaxy Tool "rglasso" run at 18/02/2015 22:06:08
cox images and outputs
(Click on a thumbnail image to download the corresponding original PDF image)
cox log output
[1] @@@ Cox model will be predicted at times = 3.724234,1325.40516225,2373.090418,3650.1730825,4989.405682
[1] Times each predictor was selected in CV models (excluding zero count predictors)
hits_lambda_1se hits_lambda_min
rhubarb 10 10
vegemite 6 6
[1] @@@ Results preview:
regulator partial_likelihood forced_in glmnet_model best_lambda lambdaChoice alpha
rhubarb rhubarb 0.0012215 TRUE cox 0.04197 lambda.1se 0.95
rglasso log output
Loading required package: Matrix
Loading required package: methods
Loaded glmnet 1.9-8
Loaded lars 1.2
Loading required package: splines
Warning messages:
1: In if (is.na(predict_at)) { :
the condition has length > 1 and only the first element will be used
2: In if (class(p) == "try-error") { :
the condition has length > 1 and only the first element will be used
3: In plot.window(...) : "label" is not a graphical parameter
4: In plot.xy(xy, type, ...) : "label" is not a graphical parameter
5: In axis(side = side, at = at, labels = labels, ...) :
"label" is not a graphical parameter
6: In axis(side = side, at = at, labels = labels, ...) :
"label" is not a graphical parameter
7: In box(...) : "label" is not a graphical parameter
8: In title(...) : "label" is not a graphical parameter
Other log output
## Toolfactory running rglasso as Rscript script
[1] @@@ Using alpha = 0.95 for all models
[1] @@@@ Input has 500 samples and 3 predictors
[1] @@@ Cox model will predict yvar= status using cols= rhubarb,vegemite,apple n preds= 3 forced in= rhubarb
[1] @@@ SessionInfo for this R session:
R version 3.1.0 (2014-04-10)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 LC_PAPER=en_AU.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] splines methods stats graphics grDevices utils datasets base
other attached packages:
[1] pec_2.4.4 survival_2.37-7 lars_1.2 glmnet_1.9-8 Matrix_1.1-5
loaded via a namespace (and not attached):
[1] codetools_0.2-10 foreach_1.4.2 grid_3.1.0 iterators_1.0.7 lattice_0.20-29 lava_1.3 prodlim_1.5.1
Warning messages:
1: In if (is.na(predict_at)) { ... :
the condition has length > 1 and only the first element will be used
2: In if (class(p) == "try-error") { ... :
the condition has length > 1 and only the first element will be used
3: In plot.window(...) : "label" is not a graphical parameter
4: In plot.xy(xy, type, ...) : "label" is not a graphical parameter
5: In axis(side = side, at = at, labels = labels, ...) :
"label" is not a graphical parameter
6: In axis(side = side, at = at, labels = labels, ...) :
"label" is not a graphical parameter
7: In box(...) : "label" is not a graphical parameter
8: In title(...) : "label" is not a graphical parameter
All output files available for downloading