utilization_functions: Utilization functions for 'TreeSummarizedExperiment' objects

In FelixErnst/mia: Microbiome analysis

Utilization functions for TreeSummarizedExperiment objects

Description

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

Usage

getReducedDimAttribute(x, ...)

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

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)

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.

Value

The extracted element from the reducedDim attribute.

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")

# Extract feature loadings
res <- getReducedDimAttribute(tse, dimred = "NMF", name = "loadings")
res |> head()

FelixErnst/mia documentation built on April 3, 2025, 2:15 p.m.