POMA_package: Tools for Omics Data Analysis

PomaRankProd

R Documentation

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 = 1, 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. Default is 1 to include all 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 the results. Objects in the list are up_regulated (tibble) and down_regulated (tibble).

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 <- POMA::st000336 %>% # Example SummarizedExperiment object included in POMA
  PomaImpute()

## Output is a list with objects `up_regulated` (tibble with up regulated features) and `down_regulated` (tibble with down regulated features) 
## Perform on no-scaled object to avoid negative values
data %>% 
  PomaRankProd(method = "pfp")

pcastellanoescuder/POMA_package documentation built on Nov. 28, 2024, 1:23 p.m.