Retrieves a vector of features (usually genes) named by the modules they belong to. Assignment can be used to modify all or part of the vector.
Usage
# S4 method for class 'ModularExperiment'
assignments(object, as_list = FALSE)
# S4 method for class 'ModularExperiment'
assignments(object) <- valueArguments
- object
ModularExperiment object.
- as_list
If
TRUE, the results are returned as a list, with an entry for each module containing a list of features.- value
New value to replace existing assignments.
Value
A vector with values representing features and names representing feature assignments (i.e., modules).
Examples
# Create ModularExperiment with random data (100 features, 50 samples,
# 10 modules)
me <- ReducedExperiment:::.createRandomisedModularExperiment(100, 50, 10)
me
#> class: ModularExperiment
#> dim: 100 50 10
#> metadata(0):
#> assays(1): normal
#> rownames(100): gene_1 gene_2 ... gene_99 gene_100
#> rowData names(0):
#> colnames(50): sample_1 sample_2 ... sample_49 sample_50
#> colData names(0):
#> 10 components
# Assignment of features to groups/modules
assignments(me)
#> module_6 module_3 module_6 module_5 module_1 module_7 module_8
#> "gene_1" "gene_2" "gene_3" "gene_4" "gene_5" "gene_6" "gene_7"
#> module_2 module_5 module_6 module_10 module_7 module_5 module_1
#> "gene_8" "gene_9" "gene_10" "gene_11" "gene_12" "gene_13" "gene_14"
#> module_1 module_6 module_9 module_8 module_2 module_5 module_8
#> "gene_15" "gene_16" "gene_17" "gene_18" "gene_19" "gene_20" "gene_21"
#> module_9 module_7 module_3 module_4 module_8 module_10 module_5
#> "gene_22" "gene_23" "gene_24" "gene_25" "gene_26" "gene_27" "gene_28"
#> module_4 module_7 module_7 module_7 module_7 module_6 module_3
#> "gene_29" "gene_30" "gene_31" "gene_32" "gene_33" "gene_34" "gene_35"
#> module_10 module_6 module_10 module_6 module_2 module_4 module_9
#> "gene_36" "gene_37" "gene_38" "gene_39" "gene_40" "gene_41" "gene_42"
#> module_2 module_5 module_9 module_6 module_6 module_9 module_6
#> "gene_43" "gene_44" "gene_45" "gene_46" "gene_47" "gene_48" "gene_49"
#> module_7 module_5 module_3 module_7 module_1 module_6 module_8
#> "gene_50" "gene_51" "gene_52" "gene_53" "gene_54" "gene_55" "gene_56"
#> module_3 module_9 module_2 module_3 module_4 module_2 module_8
#> "gene_57" "gene_58" "gene_59" "gene_60" "gene_61" "gene_62" "gene_63"
#> module_8 module_5 module_2 module_1 module_2 module_7 module_7
#> "gene_64" "gene_65" "gene_66" "gene_67" "gene_68" "gene_69" "gene_70"
#> module_6 module_9 module_5 module_8 module_6 module_2 module_10
#> "gene_71" "gene_72" "gene_73" "gene_74" "gene_75" "gene_76" "gene_77"
#> module_5 module_3 module_4 module_9 module_4 module_3 module_9
#> "gene_78" "gene_79" "gene_80" "gene_81" "gene_82" "gene_83" "gene_84"
#> module_6 module_2 module_4 module_7 module_3 module_6 module_9
#> "gene_85" "gene_86" "gene_87" "gene_88" "gene_89" "gene_90" "gene_91"
#> module_7 module_9 module_10 module_5 module_9 module_9 module_4
#> "gene_92" "gene_93" "gene_94" "gene_95" "gene_96" "gene_97" "gene_98"
#> module_6 module_7
#> "gene_99" "gene_100"
# We can reassign a feature to a new module if we like:
names(assignments(me))[6] <- "new_module"
assignments(me)[1:10]
#> module_6 module_3 module_6 module_5 module_1 new_module module_8
#> "gene_1" "gene_2" "gene_3" "gene_4" "gene_5" "gene_6" "gene_7"
#> module_2 module_5 module_6
#> "gene_8" "gene_9" "gene_10"
# We shouldn't, however, attempt to change the feature names here:
# assignments(me)[5] <- "modified_gene_name"
# Instead, we should change the object's feature names as so:
featureNames(me)[5] <- "modified_gene_name"
assignments(me)[1:10]
#> module_6 module_3 module_6
#> "gene_1" "gene_2" "gene_3"
#> module_5 module_1 new_module
#> "gene_4" "modified_gene_name" "gene_6"
#> module_8 module_2 module_5
#> "gene_7" "gene_8" "gene_9"
#> module_6
#> "gene_10"