metTest: Univariate hypothesis testing

In ethevenot/metabolis: Metabolomics Data Analysis

Description

Provides numerical metrics and graphical overview of an ExpressionSet instance

Provides numerical metrics and graphical overview of an ExpressionSet instance

Usage

metTest(x, ...)

## S4 method for signature 'MultiDataSet'
metTest(x, factorC, testC = c("param",
  "nonparam", "ttest", "limma", "wilcoxon", "anova", "kruskal", "pearson",
  "spearman")[2], adjustC = c("holm", "hochberg", "hommel", "bonferroni",
  "BH", "BY", "fdr", "none")[5], adjustThreshN = 0.05, fig.pdfC = NA,
  info.txtC = NA)

## S4 method for signature 'ExpressionSet'
metTest(x, factorC, testC = c("param",
  "nonparam", "ttest", "limma", "wilcoxon", "anova", "kruskal", "pearson",
  "spearman")[2], adjustC = c("holm", "hochberg", "hommel", "bonferroni",
  "BH", "BY", "fdr", "none")[5], adjustThreshN = 0.05, fig.pdfC = NA,
  plotMainC = NA, info.txtC = NA)

Arguments

x	An S4 object of class MultiDataSet
factorC	Character: Factor of interest (name of a column from the pData(x))
testC	Character: One of the 6 available hypothesis tests can be selected (either 'ttest', 'limma', 'wilcoxon', 'anova', 'kruskal', 'pearson', or 'spearman'); if set to 'param' (or 'nonparam' [default]), the appropriate (non-)parametric test will be used
adjustC	Character: Name of the method for correction of multiple testing (the p.adjust function is used)
adjustThreshN	Numeric: Threshold for (corrected) p-values
fig.pdfC	Character: Name of the file for the graphics from the significant features; if NA, the graphics are displayed on the screen; if NULL, no plot is generated
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
plotMainC	character: title to be displayed on the first plot
x	An S4 object of class ExpressionSet
factorC	Character: Factor of interest (name of a column from the pData(x))
testC	Character: One of the 6 available hypothesis tests can be selected (either 'ttest', 'limma', 'wilcoxon', 'anova', 'kruskal', 'pearson', or 'spearman'); if set to 'param' (or 'nonparam' [default]), the appropriate (non-)parametric test will be used
adjustC	Character: Name of the method for correction of multiple testing (the p.adjust function is used)
adjustThreshN	Numeric: Threshold for (corrected) p-values
fig.pdfC	Character: Name of the file for the graphics from the significant features; if NA, the graphics are displayed on the screen; if NULL, no plot is generated
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 adjusted p-values in the fData data frames

ExpressionSet including the adjusted p-values in fData (or the vector of adjusted p-values when returnAdjustOnlyL is TRUE)

Examples

prometMset <- metRead(system.file("extdata/promet", package="metabolis"))
prometMset <- metTest(prometMset, "gene")
sacSet <- metRead(system.file("extdata/sacurine", package="metabolis"))
sacSet <- metCorrect(sacSet)
sacSet <- metTransform(sacSet)
sacSet <- metTest(sacSet, "gender", "ttest")

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