PomaRankProd: Rank Product/Rank Sum Analysis for Mass Spectrometry Data

Description Usage Arguments Value Author(s) References

View source: R/PomaRankProd.R

Description

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

Usage

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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


pcastellanoescuder/POMA documentation built on May 14, 2021, 11:07 p.m.