MAMA (version 2.1.0)

metaMA: Wrapper function for effect size or p-value combination methods

Description

This is a wrapper function for effect size or p-value combination as implemented in metaMA package.

Usage

metaMA(data, varname, moderated = c("limma", "SMVar", "t")[1], BHth = 0.05, which = c("pval", "ES")[1])

Arguments

data

MetaArray object

varname

Character String - name of one column in clinical data matrices to be used as class labels

moderated

Character - method to calculate the test statistic (or p-value) inside each study, one of: "limma", "SMVar" and "t"

BHth

Numeric - threshold for Benjamini Hochenberg adjusted p-values for selection of significant genes in meta-analysis

which

Character - choose "pval" for combination of p-values, or "ES" for effect sizes

Value

• An object of class "metaMA.res". It is a list where:
• Study1
  Vector of indices of differentially expressed genes in study 1. Similar names are given for the other individual studies.
• AllIndStudies
  Vector of indices of differentially expressed genes found by at least one of the individual studies.
• Meta
  Vector of indices of differentially expressed genes in the meta-analysis.
• TestStatistic
  Vector with test statistics for differential expression in the meta-analysis.

References

Marot, G., Foulley, J.-L., Mayer, C.-D., Jaffrezic, F. Moderated effect size and p-value combinations for microarray meta-analyses.

See Also

pvalcombination, EScombination

Examples

data(ColonData)
pv<-metaMA(ColonData, "satelite", moderated = "t")