Generics for Embbedding Results into a SummarizedExperiment Object

An overview of the generics for embedding results into a SummarizedExperiment object, in a format compatible with iSEEde.

Usage

embedContrastResults(x, se, name, ...)

embedContrastResultsMethods

# S4 method for class 'ANY'
embedContrastResults(x, se, name, ...)

# S4 method for class 'data.frame'
embedContrastResults(x, se, name, class, ...)

Format

embedContrastResultsMethods: Named character vector mapping keywords to class names designed to store differential expression results.

Arguments

x

Object to be embedded.

se

A SummarizedExperiment object.

name

Identifier for the embedded object.

...

Arguments passed to and from other methods.

class

Class to use for embedding x. Only used when class(x) does not uniquely identify the package that generated the object.

Value

An updated SummarizedExperiment object that contains the embedded object.

Definitions

• embedContrastResults(x, se, name, ...) embeds the results x in the SummarizedExperiment se.

Author

Kevin Rue-Albrecht

Examples

embedContrastResultsMethods
#>              limma 
#> "iSEELimmaResults" 

showMethods(embedContrastResults)
#> Function: embedContrastResults (package iSEEde)
#> x="ANY"
#> x="DESeqResults"
#> x="TopTags"
#> x="data.frame"
#> x="iSEEDESeq2Results"
#> x="iSEELimmaResults"
#> x="iSEEedgeRResults"
#>