Creates a GO feature MSnSet

Creates a new "MSnSet" instance populated with a GO term binary matrix based on an original object.

Usage

makeGoSet(object, params, namespace = "cellular_component", evidence = NULL)

Arguments

object

An instance of class "MSnSet" or a character of feature names.

params

An instance of class "AnnotationParams", compatible with featureNames(object)'s format.

namespace

The ontology name space. One or several of "biological_process", "cellular_component" or "molecular_function".

evidence

GO evidence filtering.

Value

A new "MSnSet" with the GO terms for the respective features in the original object.

Author

Laurent Gatto

Examples

library("pRolocdata")
data(dunkley2006)
data(dunkley2006params)
goset <- makeGoSet(dunkley2006[1:10, ],
                   dunkley2006params)
goset
#> MSnSet (storageMode: lockedEnvironment)
#> assayData: 10 features, 2 samples 
#>   element names: exprs 
#> protocolData: none
#> phenoData: none
#> featureData
#>   featureNames: AT1G09210 AT1G21750 ... AT1G07810 (10 total)
#>   fvarLabels: assigned evidence ... markers (8 total)
#>   fvarMetadata: labelDescription
#> experimentData: use 'experimentData(object)'
#> Annotation:  
#> - - - Processing information - - -
#> Constructed GO set using cellular_component namespace [Fri Oct 18 17:20:19 2024] 
#>  MSnbase version: 2.31.1 
exprs(goset)
#>           GO:0005783 GO:0005788
#> AT1G09210          0          0
#> AT1G21750          1          1
#> AT1G51760          0          0
#> AT1G56340          1          1
#> AT2G32920          0          0
#> AT2G47470          1          0
#> AT3G54960          0          0
#> AT4G24190          0          1
#> AT5G60640          1          1
#> AT1G07810          0          0
image(goset)