SAM.Anal: SAM analysis

In flajole/MApckg: R package of MetaboAnalyst functions

Description

Perform Significance Analysis of Microarray (and Metabolites). Uses sam function.

Usage

SAM.Anal(dataSet, analSet, method = "d.stat", paired = FALSE,
  var.equal = TRUE)

Arguments

dataSet	List, data set object generated by MS_to_MA function.
analSet	List, containing the results of statistical analysis (can be just an empty list).
method	A character string or a name specifying the method/function that should be used in the computation of the expression scores d. If "d.stat", a modified t-statistic or F-statistic, respectively, will be computed as proposed by Tusher et al. (2001). If "wilc.stat", a Wilcoxon rank sum statistic or Wilcoxon signed rank statistic will be used as expression score.
paired	Are values in data set paired or not.
var.equal	Are variances assumed equal or not.

Value

Native analSet with one added $sam element containing standard sam function output

See Also

sam for used statistical functions
SetSAMSigMat for setting matrix of significance
PlotSAM for plotting functions

flajole/MApckg documentation built on May 16, 2019, 1:16 p.m.