Download an MCA dataset archive, or read a locally available ZIP archive, and import the requested metadata or expression table.
Arguments
- url
URL of an MCA ZIP archive (for example, one returned by
listMCA()), or the path to a local ZIP archive.- type
Character string specifying the table to import:
"data"(cell metadata; default),"exp"(processed expression values), or"raw"(raw counts).- timeout
Download timeout in seconds (default: 300). This applies only to remote URLs; the previous R timeout option is restored on exit.
Value
A data.frame containing the selected table, with the first CSV
column used as row names. For expression tables, genes are expected to
occupy rows and cells columns, as provided by the MCA download.
Details
Only the requested CSV file is extracted, into an isolated
temporary directory. Temporary files are removed when the function exits,
including if an error occurs. Local input ZIP archives are never deleted.
The supported archive members end in -data.csv, -exp.csv, or
-raw.csv (also accepting underscore separators and .csv.gz).
Examples
if (FALSE) { # \dontrun{
url <- "https://www.malariacellatlas.org/downloads/pf-ch10x-set4-biorxiv.zip"
metadata <- easyMCA(url, type = "data")
expression <- easyMCA(url, type = "exp")
raw_counts <- easyMCA(url, type = "raw")
# An already downloaded archive can also be used offline.
metadata <- easyMCA("path/to/pf-ch10x-set4-biorxiv.zip", "data")
# When creating a Seurat object, check that cells match and
# convert the counts data frame to a numeric matrix.
stopifnot(all(colnames(raw_counts) %in% rownames(metadata)))
seurat_obj <- Seurat::CreateSeuratObject(
counts = as.matrix(raw_counts),
meta.data = metadata[colnames(raw_counts), , drop = FALSE],
project = "MCA"
)
} # }