as.BiocContainer: Converts a "facile result" to a traditional Bioconductor...

In facileverse/FacileData: A fluent API for accessing multi-assay high-throughput genomics data

Converts a "facile result" to a traditional Bioconductor assay container.

Description

An entire FacileDataSet or a subset of it can be converted into bioconductor-standard assay containers, like a SummarizedExperiment, DGEList, or ExpressionSet "at any time" using various as.XXX functions, like as.DGEList(...).

Usage

as.DGEList(x, ...)

## S3 method for class 'data.frame'
as.DGEList(
  x,
  covariates = TRUE,
  feature_ids = NULL,
  assay_name = NULL,
  .fds = NULL,
  custom_key = Sys.getenv("USER"),
  ...
)

## S3 method for class 'tbl'
as.DGEList(
  x,
  covariates = TRUE,
  feature_ids = NULL,
  assay_name = NULL,
  .fds = NULL,
  custom_key = Sys.getenv("USER"),
  ...
)

## S3 method for class 'facile_frame'
as.DGEList(
  x,
  covariates = TRUE,
  feature_ids = NULL,
  assay_name = NULL,
  custom_key = Sys.getenv("USER"),
  ...
)

## S3 method for class 'FacileDataSet'
as.DGEList(
  x,
  covariates = TRUE,
  feature_ids = NULL,
  assay_name = NULL,
  custom_key = Sys.getenv("USER"),
  ...
)

as.ExpressionSet(x, ...)

## S3 method for class 'data.frame'
as.ExpressionSet(
  x,
  covariates = TRUE,
  feature_ids = NULL,
  assay_name = default_assay(.fds),
  .fds = fds(x),
  custom_key = Sys.getenv("USER"),
  ...
)

## S3 method for class 'FacileDataSet'
as.ExpressionSet(
  x,
  covariates = TRUE,
  feature_ids = NULL,
  assay_name = default_assay(.fds),
  .fds = fds(x),
  custom_key = Sys.getenv("USER"),
  ...
)

as.SummarizedExperiment(x, ...)

## S3 method for class 'data.frame'
as.SummarizedExperiment(
  x,
  covariates = TRUE,
  feature_ids = NULL,
  assay_name = default_assay(.fds),
  .fds = fds(x),
  custom_key = Sys.getenv("USER"),
  ...
)

## S3 method for class 'FacileDataSet'
as.SummarizedExperiment(
  x,
  covariates = TRUE,
  feature_ids = NULL,
  assay_name = default_assay(.fds),
  .fds = fds(x),
  custom_key = Sys.getenv("USER"),
  ...
)

Arguments

x	a facile expression-like result
covariates	The covariates the user wants to add to the $samples of the DGEList. This can take the following forms: TRUE: All covariates are retrieved from the FacileDataSet FALSE: TODO: Better handle FALSE character: A vector of covariate names to fetch from the FacileDataSet. Must be elements of names(sample_definitions(x)) data.frame: A wide covariate table (dataset, sample_id, covariates ...) This may be external covariates for samples not available within x (yet), ie. a table of covariates provided by a third party. NULL: do not decorate with any covariates.
feature_ids	the features to get expression for (if not specified in x descriptor). These correspond to the elements found in the feature_info_tbl(x)$feature_id column.
assay_name	the name of the assay matrix to use when populating the default assay matrix of the bioconductor container (the ⁠$counts⁠ matrix of a DGEList, the exprs() of an ExpressionSet, etc.). The default value is the entry provided by default_assay()
.fds	The FacileDataSet that x was retrieved from
custom_key	the custom key to use to fetch custom annotations from .fds

Details

We use the term "facile object" to refer to either the entirety of a FacileDataStore or any sample-descriptor that specifies subsets of the data, eg. where fds(x) returns a FacileDataStore. See examples for specifics.

Note that the order that the samples and features are materialized into the expression container are not guaranteed.

Value

the appropriate bioconductor assay container, ie. an edgeR::DGEList for as.DGEList, a Biobase::ExpressionSet for as.ExpressionSet, or a SummarizedExperiment::SummarizedExperiment for as.SummarizedExperiment.

a ExpressionSet

a SummarizedExperiment

Examples

fds <- exampleFacileDataSet()

# Retrieve DGEList of gene expression for all samples
y.all <- as.DGEList(fds) # gene expression of all samples

# Retrieve data for only 3 genes
# Suppose we only wanted female samples in our DGEList
y.fem <- fds |>
  filter_samples(sex == "f") |>
  as.DGEList() # or as.ExpressionSet()

facileverse/FacileData documentation built on Feb. 24, 2024, 7:59 a.m.