download-expression-matrices: Download Expression Matrices with HCAExplorer

In Bioconductor/HCAExplorer: Browse the Human Cell Atlas data portal

Description

Methods used to download expression matrices availiable through the HCA Data Portal. The method 'checkExpressionMatricesAvaiability' specifies whether expression matrices can be downloaded for a project. The method 'downloadExpressionMatrices' downloads and returns expression matrices in a variety of formats.

Usage

checkExpressionMatricesAvailability(x, ...)
 downloadExpressionMatrices(x, ...)

## S4 method for signature 'HCAExplorer'
checkExpressionMatricesAvailability(
  x,
  format = c("loom", "csv", "mtx"),
  organism
)

## S4 method for signature 'HCAExplorer'
downloadExpressionMatrices(
  x,
  format = c("loom", "csv", "mtx"),
  organism,
  useBiocFileCache = TRUE
)

Arguments

x	an HCAExplorer object. All project entries in the object will attempt to be downloaded. Use subsetting to reduce the projects that are to be downloaded.
format	either "loom", "csv", of "mtx". The default value is "loom". Which format the expression matrices should be downloaded as. If "loom", a 'LoomExperiment' object will be returned. If "csv", a tibble will be returned. If "mtx", a 'SingleCellExperiment' object will be returned.
organism	character(1). Which organism file to download. Usually either "Homo sapiens" or "Mus musculus". If not specified, all organism files will be included in the download.
useBiocFileCache	logical(1). Whether to save file with 'BiocFileCache'. Defaults to 'TRUE'. If 'TRUE', 'BiocFileCache' will be used to save a persistent copy of the file to the user's computer. This persistent copy will be used instead of redownloading the expression matrices in subsequent uses. If 'FALSE', the file will be saved to a temporary directory and will be removed when the session ends.
...	Additional arguments.

Value

For 'checkExpressionMatrixAvailability', returns a tibble. For ‘downloadExpressionMatrices’, returns a list of downloaded expression matrices in a format specified by the 'format' argument.

Author(s)

Daniel Van Twisk

Examples

hca <- HCAExplorer()
checkExpressionMatricesAvailability(hca)

hca <- hca[5]
hca <- downloadExpressionMatrices(hca, useBiocFileCache = FALSE)

Bioconductor/HCAExplorer documentation built on Feb. 13, 2021, 7:07 a.m.