metView: Viewing the MultiDataSet object.

In ethevenot/metabolis: Metabolomics Data Analysis

Description

Provides numerical metrics and graphical overview of each dataset

Provides numerical metrics and graphical overview of an ExpressionSet instance

Usage

metView(x, ...)

## S4 method for signature 'MultiDataSet'
metView(x, factorC = NA, fig.pdfC = NA,
  poolAsPool1L = FALSE, poolCvN = 0.3, univTestC = "nonparam",
  univAdjustC = "BH", univThreshN = 0.05, plotMainC = "",
  plotOverviewL = TRUE, plotSpanN = 1,
  plotSampIntensityC = c("median", "mean")[1], info.txtC = NA)

## S4 method for signature 'ExpressionSet'
metView(x, factorC = NA, fig.pdfC = NA,
  poolAsPool1L = FALSE, poolCvN = 0.3, univTestC = "nonparam",
  univAdjustC = "BH", univThreshN = 0.05, plotMainC = NA,
  plotSpanN = 1, plotSampIntensityC = c("median", "mean")[1],
  info.txtC = NA)

Arguments

x	MultiDataSet: multiple dataset to be explored
factorC	Character: column name of pData to be used for sample color and univariate test
fig.pdfC	Character: Name of the file for the graphics; if NA, the graphics are displayed on the screen;
poolAsPool1L	Logical: should pool be included (as pool1) in the correlation with the dilution factor?
poolCvN	Numeric: threshold for the coefficient of variation of the pools
univTestC	Character: if 'factorC' is specified, which test should be used (see the univariate method)
univAdjustC	Character: if 'factorC' is specified, which correction for multiple testing should be used (see the univariate method)
plotMainC	Character: title; note that all 'plot' parameters are used only for display
plotOverviewL	Logical: should an overview of the number of samples and variables in all datasets be barplotted?
plotSpanN	Numeric: span parameter used in the loess trend estimation
plotSampIntensityC	Character: function to be used to display the global sample intensity
info.txtC	Character: File name for the printed results (call to 'sink()'); if NA (default), messages will be printed on the screen; if NULL, no verbose will be generated
univTreshN	Character: if 'factorC' is specified, which threshold for the corrected p-values should be used to reject the null hypothesis?
x	ExpressionSet: dataset to be explored
factorC	Character: column name of pData to be used for sample color and univariate test
fig.pdfC	Character: name of the pdf file for output
poolAsPool1L	Logical: should pool be included (as pool1) in the correlation with the dilution factor?
poolCvN	Numeric: threshold for the coefficient of variation of the pools
univTestC	Character: if 'factorC' is specified, which test should be used (see the univariate method)
univAdjustC	Character: if 'factorC' is specified, which correction for multiple testing should be used (see the univariate method)
univTreshN	Character: if 'factorC' is specified, which threshold for the corrected p-values should be used to reject the null hypothesis?
plotMainC	Character: title; note that all 'plot' parameters are used only for display
plotSpanN	Numeric: span parameter used in the loess trend estimation
plotSampIntensityC	Character: function to be used to display the global sample intensity
info.txtC	Character: File name for the printed results (call to 'sink()'); if NA (default), messages will be printed on the screen; if NULL, no verbose will be generated

Value

MultiDataSet including the computed sample and variable metrics

ExpressionSet including the computed sample and variable metrics

Examples

prometMset <- metRead(system.file("extdata/promet",
                                  package = "metabolis"))
## Not run: 
prometMset <- metView(prometMset)
prometMset <- metView(prometMset, factorC = "gene")

## End(Not run)

sacSet <- metRead(system.file("extdata/sacurine",
                              package = "metabolis"))
sacSet <- metView(sacSet)
sacSet <- metCorrect(sacSet)
sacSet <- metView(sacSet)
sacSet <- metTransform(sacSet)
sacSet <- metView(sacSet)
sacSet <- metView(sacSet, factorC = "gender")

ethevenot/metabolis documentation built on June 28, 2019, 1:27 p.m.