Utilization functions for TreeSummarizedExperiment objects

A set of utility functions designed to facilitate operations with TreeSummarizedExperiment objects

getReducedDimAttribute(x, ...)

convertToMAE(x, ...)

convertToTreeSE(x, ...)

# S4 method for class 'SingleCellExperiment'
getReducedDimAttribute(x, dimred = 1L, name = NULL, ...)

# S4 method for class 'SingleCellExperiment'
convertToMAE(x, ...)

# S4 method for class 'MultiAssayExperiment'
convertToTreeSE(x, ...)

Arguments

x

a SummarizedExperiment object.

...

additional arguments, not used currently.

dimred

Character scalar or integer scalar. A name or index of dimension reduction results. (Default: 1L)

name

Character vector. A name of values retrieved from attributes of reducedDim(x, dimred). If NULL, all the values are retrieved. (Default: NULL)

Value

The extracted element from the reducedDim attribute.

Details

getReducedDimAttribute is a utility function that retrieves specific elements from the attributes of reducedDim in a TreeSummarizedExperiment object. These attributes may contain loadings, statistical test results, or other metadata, depending on the methods used to generate the results.

See also

runCCA, addNMF, and addLDA

Examples

data(GlobalPatterns)
tse <- GlobalPatterns

# Reduce the number of features
tse <- agglomerateByPrevalence(tse, rank = "Phylum")

# Run NMF and add the result to reducedDim(tse, "NMF").
tse <- addNMF(tse, k = 1, name = "NMF")
#> NMF - BioConductor layer [OK] | Shared memory capabilities [NO: bigmemory] | Cores 2/2
#>   To enable shared memory capabilities, try: install.extras('
#> NMF
#> ')
#> 
#> Attaching package: ‘NMF’
#> The following object is masked from ‘package:S4Vectors’:
#> 
#>     nrun
#> The following object is masked from ‘package:generics’:
#> 
#>     fit

# Extract feature loadings
res <- getReducedDimAttribute(tse, dimred = "NMF", name = "loadings")
res |> head()
#>                         [,1]
#> AD3             8.402178e-04
#> Acidobacteria   3.118431e-02
#> Actinobacteria  1.202791e-01
#> Armatimonadetes 4.525469e-04
#> BRC1            6.081208e-05
#> Bacteroidetes   2.861651e-01

# Convert MultiAssayExperiment to TreeSE
data(HintikkaXOData)
convertToTreeSE(HintikkaXOData)
#> class: TreeSummarizedExperiment 
#> dim: 12706 40 
#> metadata(0):
#> assays(1): counts
#> rownames(12706): GAYR01026362.62.2014 CVJT01000011.50.2173 ...
#>   JRJTB:03787:02429 JRJTB:03787:02478
#> rowData names(7): Phylum Class ... Species OTU
#> colnames(40): C1 C2 ... C39 C40
#> colData names(6): Sample Rat ... Fat XOS
#> reducedDimNames(0):
#> mainExpName: microbiota
#> altExpNames(2): metabolites biomarkers
#> rowLinks: NULL
#> rowTree: NULL
#> colLinks: NULL
#> colTree: NULL