addFacileAssaySet: Adds new set of assay data for all samples in a FacileDataSet

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

Adds new set of assay data for all samples in a FacileDataSet

Description

Once a FacileDataSet has been created and initialized, either via a low-level call to initializeFacileDataSet(), or a call to as.FacileDataSet() over a list of BiocAssayContainers, you can add more assays (i.e. RNA-seq, microarray, etc.) to the FacileDataSet using this function.

Usage

addFacileAssaySet(
  x,
  datasets,
  facile_assay_name,
  facile_assay_type = .assay.types,
  facile_feature_type = NULL,
  facile_assay_description = NULL,
  facile_feature_info,
  storage_mode = .storage.modes,
  chunk_rows = 5000,
  chunk_cols = "ncol",
  chunk_compression = 4,
  assay_name = NULL,
  warn_existing = FALSE,
  add_sample_covariates = TRUE,
  covariate_def = NULL
)

Arguments

x	The FacileDataSet
datasets	list of ExpressionSet, SummarizedExperiment, or DGELists that have the new assay data across all of the datasets in x.
facile_assay_name	the name of the assay in the source dataset object
facile_assay_type	string indicating the assay_type ('rnaseq', 'affymetrix', etc.)
facile_feature_type	a string indicating the universe the features in this can be anything, but certain identifiers are special like "entrez", "ensgid", "enstid", etc.
facile_feature_info	a data.frame with the required feature_info columns that describe the features in this assay. Please refer to the "Features" section of the FacileDataSet vignette for more complete description.
storage_mode	either "integer" or "numeric", maps to the storage.mode parameter in rhdf5::h5createDataset()
chunk_rows	the first entry in the chunk parameter in rhdf5::h5createDataset() (integer)
chunk_cols	the second entry in the chunk parameter in rhdf5::h5createDataset(). If this is "ncol", it is set to the number of columns in each of the internal dataset matrices being added.
chunk_compression	the level parameter in rhdf5::h5createDataset()
assay_name	the assay name in the data containers provided in the datasets list.
facie_assay_description	a string that allows the caller to provide a "freeform" description of the assay (platform, protocol, whatever).

Details

Note that you cannot add assay data piecemeal. That is to say, you can not call this function once to add copynumber data (addFacileAssaySet(..., facile_assay_type = "cnv") to a subset of samples and later call this function again to add copynumber to the rest of the samples. The function will throw an error if facile_assay_type %in% assay_names(x) == TRUE.

Value

a tibble subset of facile_feature_info that indicates the new features that were added to the internal feature_info_tbl.

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