loadHCAMatrix: Obtain expression matrix data from the Human Cell Atlas API...

In Bioconductor/HCAMatrixBrowser: Extract and manage matrix data from the Human Cell Atlas project

Obtain expression matrix data from the Human Cell Atlas API service

Description

Using a vector of data bundle identifiers ('bundle_fqids'), users can request the associated matrix of expression values. The query submitted by 'loadHCAMatrix' may take some time to be completed. Once the query is completed, either a 'LoomExperiment', 'SingleCellExperiment', or 'tibble' table is returned (depending on the value of 'format').

Usage

loadHCAMatrix(
  api,
  bundle_fqids,
  verbose = FALSE,
  names.col = "CellID",
  format = c("loom", "mtx", "csv"),
  feature = c("gene", "transcript")
)

Arguments

api	An API object of class 'HCAMatrix' from the 'HCAMatrix' function
bundle_fqids	character() v0 Bundle identifiers
verbose	logical (default FALSE) whether to output stepwise messages
names.col	character (default "CellID") The column name in the 'colData' metadata to use as column names of the LoomExperiment object when 'format = "loom"'
format	character(1) Data return format, one of: c("loom", "mtx", "csv"); (default: "loom")
feature	character(1) Provide either cell by "gene" or "transcript" matrices (default: "gene")

Value

A 'LoomExperiment', 'SingleCellExperiment' or 'tibble' object

Examples

hca <- HCAMatrix()

## with an bundle_fqid character vector

bundle_fqids <-
    c("ffd3bc7b-8f3b-4f97-aa2a-78f9bac93775.2019-05-14T122736.345000Z",
    "f69b288c-fabc-4ac8-b50c-7abcae3731bc.2019-05-14T120110.781000Z",
    "f8ba80a9-71b1-4c15-bcfc-c05a50660898.2019-05-14T122536.545000Z")

loadHCAMatrix(hca, bundle_fqids)

## using filtering operation

hca2 <- filter(hca, dss_bundle_fqid %in% bundle_fqids)
filters(hca2)
loadHCAMatrix(hca2)

Bioconductor/HCAMatrixBrowser documentation built on March 16, 2023, 6:16 a.m.