-
This package, in conjunction with the hca package, allows for exploration of the Human Cell Atlas' data, made available by their API.
-
Its core functionality is the generation of relational database tables containing data from
.loom
and.h5ad
files -
This is done by using the
hca
package to obtain.loom
and.h5ad
files from the HCA API, each of which can be parse into aSingleCellExperiment
object, providing us with access to (1) cell annotations, (2) gene annotations, (3) assay matrices, and (4) file metadata. -
Each of these data categories in turn corresponds to a table in the relational database schema:
- genes_tbl
- cells_tbl
- assays_tbl
- experiment_overviews
devtools::load_all()
library(hca)
library(dplyr)
- loading the two smallest
.loom
files
loom_filter <- hca::filters(fileFormat = list(is = c("loom")))
loom_tbl <- hca::files(filters = loom_filter,
size = 2, sort = "fileSize", order = "asc")
files_to_db(loom_tbl)
- loading
.loom
files produced by a single project, and processed by the HCA
filters <- filters(
fileFormat = list(is = "loom"),
fileSource = list(is = "DCP/2 Analysis")
)
files <- files(filters) # how many? 46 files
files |> # number and total size per project
group_by(projectTitle) |>
summarize(n = n(), GB = sum(size) / (1024^3)) |>
arrange(GB)
filters <- filters(
## a particular project, with 3 files, 1/2 GB
projectId = list(is = "88ec040b-8705-4f77-8f41-f81e57632f7d"),
fileFormat = list(is = "loom"),
fileSource = list(is = "DCP/2 Analysis")
)
loom_tbl <- files(filters)
files_to_db(loom_tbl)