PomaRankProd {POMA} | R Documentation

## Rank Product/Rank Sum Analysis for Mass Spectrometry Data

### Description

PomaRankProd() performs the Rank Product method to identify differential feature concentration/intensity.

### Usage

    PomaRankProd(
      data,
      logged = TRUE,
      logbase = 2,
      paired = NA,
      cutoff = 0.05,
      method = "pfp"
    )

### Arguments

`data` | A MSnSet object. First `pData` column must be the subject group/type.
`logged` | If "TRUE" (default) data have been previously log transformed.
`logbase` | Numerical. Base for log transformation.
`paired` | Number of random pairs generated in the function, if set to NA (default), the odd integer closer to the square of the number of replicates is used.
`cutoff` | The pfp/pvalue threshold value used to select features.
`method` | If cutoff is provided, the method needs to be selected to identify features. "pfp" uses percentage of false prediction, which is a default setting. "pval" uses p-values which is less stringent than pfp.

### Value

A list with all results for Rank Product analysis including tables and plots.

### Author(s)

Pol Castellano-Escuder

### References

Breitling, R., Armengaud, P., Amtmann, A., and Herzyk, P.(2004) Rank Products: A simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments, FEBS Letter, 57383-92

Hong, F., Breitling, R., McEntee, W.C., Wittner, B.S., Nemhauser, J.L., Chory, J. (2006). RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis Bioinformatics. 22(22):2825-2827

Del Carratore, F., Jankevics, A., Eisinga, R., Heskes, T., Hong, F. & Breitling, R. (2017). RankProd 2.0: a refactored Bioconductor package for detecting differentially expressed features in molecular profiling datasets. Bioinformatics. 33(17):2774-2775

[Package POMA version 1.2.0 Index]