tkWidgets (version 1.50.0)

importPhenoData: Functions to input data for an AnnotatedDataFrame object

Description

This functions allow users to read data from an existing file or an R data.frame object and use the data frame to construct an AnnotatedDataFrame object.

Usage

importPhenoData(fileName, sampleNames = NULL, from = NULL)
createPData(pdata, varList)
writePDRowNames(pdata, sampleNames)
writePhenoTable(base, textWidget, pdata)
makePhenoData(pdata)
convert2PData(phenoList)
getOBJWidget(type = NULL)
objExists(name, type = NULL)
getSNCNums(sampleNames)
getCovarDesc(varList)

Arguments

fileName

a character string for the name of a file that is going to be used to build an AnnotatedDataFrame object.

sampleNames

a vector of character strings for the names of samples. The length of sampleNames should be the same as the number of rows of an existing file or data.frame if an AnnotatedDataFrame object is to be created based on a file or data.frame.

pdata

a data.frame for the experimental data.

base

an RTcl object for the base window a widget resides.

textWidget

an RTcl object for a text box widget.

phenoList

a list of lists for tclVar() objects.

type

a character string for the class of a object e.g. data.frame, AnnotatedDataFrame.

name

a character string for the name of an object.

varList

a list of characters with names being covariate names and values being short descriptions of covariate names.

from

a character string indicating how an AnnotatedDataFrame object will be created. "file" - create from an existing file, "object" - create from an existing data frame object, "edit" - create by editing an existing AnnotatedDataFrame object, and "new" create a new AnnotatedDataFrame object from scratch. NULL or any other values for from will invoke a widget that allows users to select one of the four means from an interface.

Value

An AnnotatedDataFrame object.

Details

When import a data.frame or AnnotatedDataFrame object, the object to be imported should have been stored in .GlobelEnv. All the objects of data.frame or AnnotatedDataFrame will be made available through a browser.

The main widget if importPhenoData that calls other functions/widgets to have the job done.

Package Biobase is required for importPhenoData but the requirement id not forced as it is the only time the package is used. Users have to make sure that Biobase is available.

References

AnnotatedDataFrame class in Biobase

See Also

AnnotatedDataFrame-class

Examples

if(interactive()){
    importPhenoData()
}