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Commit message:
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ipo.xml |
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| diff -r 77d886658570 -r cfb2d8ac6797 ipo.xml --- a/ipo.xml Mon Dec 07 06:09:57 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,51 +0,0 @@ -<tool id="ipo" name="XCMS - IPO" version="0.1.0"> - <description>: A Tool for automated Optimization of XCMS Parameters</description> - <command interpreter="Rscript">ipo.R $input $html_file $html_file.files_path</command> - <inputs> - <param format="cdf" name="input" type="data" label="Source file"/> - </inputs> - <outputs> - <data format="html" name="html_file" label="ipo_output.html"/> - </outputs> - <help> -**IPO - Version 0.1** - -Version 0.1 uses the following XCMS parameters as default - -> peakpickingParameters$min_peakwidth : c(10,20) - -> peakpickingParameters$max_peakwidth : c(26,42) - -> peakpickingParameters$ppm : 20 - -> peakpickingParameters$nSlaves : 4 # as.numeric(args[3]) - -> type : "centWave" - ------ - -**IPO optimization process** - -.. image:: ${static_path}/images/ipo.jpg - :height: 400 - :width: 429 - ------ - -To optimize parameters different values (levels) have to tested for these parameters. To efficiently test many different levels design of experiment (DoE) is used. Box-Behnken and central composite designs set three evenly spaced levels for each parameter. The method 'getDefaultXcmsSetStartingParams' provides default values for the lower and upper levels defining a range. Since the levels are evenly spaced the middle level or center point is calculated automatically. To edit the starting levels of a parameter set the lower and upper level as desired. If a parameter should not be optimized, set a single default value for 'xcms' processing, do not set this parameter to NULL. - -The method 'getDefaultXcmsSetStartingParams' creates a list with default values for the optimization of the peak picking methods 'centWave' or 'matchedFilter'. To choose between these two method set the parameter accordingly. - ------ - -The method 'optimizeXcmsSet' has the following parameters: - -> **files**: the raw data which is the basis for optimization. This does not necessarly need to be the whole dataset, only quality controls should suffice. - -> **params**: a list consisting of items named according to 'xcms' peak picking methods parameters. A default list is created by 'getDefaultXcmsSetStartingParams'. - -> **nSlaves**: the number ofexperiments of an DoE processed in parallel - -> **subdir**: a directory where the response surface models are stored. Can also be NULL if no rsm's should be saved. - </help> -</tool> \ No newline at end of file |