Extract differentially expressed miRNAs and genes from a MirnaExperiment object

The mirnaDE() and geneDE() are two accessor functions for the mirnaDE and geneDE slots of MirnaExperiment class, respectively. Thus, they can be used to explore the results of miRNA and gene differential expression analysis stored in a MirnaExperiment object.

Usage

mirnaDE(object, onlySignificant = TRUE, param = FALSE, returnObject = FALSE)

geneDE(object, onlySignificant = TRUE, param = FALSE, returnObject = FALSE)

Arguments

object

A MirnaExperiment object containing miRNA and gene data

onlySignificant

Logical, if TRUE differential expression results will be returned just for statistically significant miRNAs/genes, if FALSE the full table of miRNA/gene differential expression will be provided. Default is TRUE to only report significant miRNAs/genes

param

Logical, whether to return the complete list object with the parameters used, or just the results stored in data. Default is FALSE

returnObject

Logical, if TRUE this function will return the limma/edgeR/DESeq2 object used for differential expression analysis

Value

A data.frame with miRNA/gene differential expression, or a list object with the parameters used if param = TRUE.

Functions

• mirnaDE(): Extract miRNA differential expression results

• geneDE(): Extract gene differential expression results

Author

Jacopo Ronchi, jacopo.ronchi@unimib.it

Examples

# load example MirnaExperiment object
obj <- loadExamples()

# access miRNA differential expression of a MirnaExperiment object
sig <- mirnaDE(obj)
all <- mirnaDE(obj, onlySignificant = FALSE)

# access gene differential expression of a MirnaExperiment object
sig <- geneDE(obj)
all <- geneDE(obj, onlySignificant = FALSE)