PomaRankProd: Rank Product/Rank Sum Analysis

In pcastellanoescuder/POMA: Tools for Omics Data Analysis

Rank Product/Rank Sum Analysis

Description

PomaRankProd performs the Rank Product (or Rank Sum) method to identify differentially expressed genes.

Usage

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

Arguments

data	A SummarizedExperiment object.
logged	Logical. Indicates if data should be log transformed first.
paired	Numeric. Indicates the 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	Numeric. Indicates the pfp/pvalue threshold value used to select features.
method	Character. Indicates the method 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 results including plots and tables.

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

Examples

data("st000336")

st000336 %>% 
  PomaImpute() %>%
  PomaRankProd()

pcastellanoescuder/POMA documentation built on March 15, 2024, 10:08 p.m.