| normalization {StabPerf} | R Documentation |
Calls several normalization routines on a given data set. All options are defined in a configuration file, which is in R syntax.
normalization(file=NULL, config=getOption("edaprakt.normalize"))
file |
character. Path to data file (*.RData file). This object saved in this file should have its data (as a data.frame or matrix) stored in the field $x and its factors/labels stored in the field $y. |
config |
character. Path to configuration file. |
The configuration file is in R syntax and contains blocks of code sourrounded by {} and \code{}. Each block is considered a single normalization routine. In each block, the variable data contains whatever is loaded from the file which is provided. If no file is provided, the name of the file stored in the option edaprakt.rawfile is read and its contents are saved in the variable data. Generally this should be a list, containing the data itself, plus a field containing the factors for the data.
These blocks of code may return normalized data, in which case the results of all the normalization routines are returned in a list from this function. Many normalization routines may simply choose to call doPlots on their normalized results, without returning any data to this function. (See doPlots).
For further details on parsing the configuration file, see confParser.
Classes of the data may also be grouped before the normalization by setting the options edaprakt.normalize.classes.set and edaprakt.normalize.classes.combine (See changeLabels).
Outlier samples may be removed before the normalization by setting the option edaprakt.outliers to a list of sample indices (column indices) to be excluded.
In order to visualize the results of a normalization routines, see doPlots.
list |
Whatever is returned from the blocks of code in the configuration file |
confParser, smad, centralize, parallel.loess, doPlots, changeLabels
normalization(file='data/my_raw_data.RData', config='path/to/normalize.conf') # Configuration file examples can be found in the this-is-escaped-codenormal-bracket6bracket-normal directory of this package.