import: Import Human Cell Atlas '.mtx.zip' or '.loom' archives

Description Usage Arguments Value Examples

Description

Import Human Cell Atlas '.mtx.zip' or '.loom' archives

Usage

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import_loom(.data, path, ..., verbose = FALSE)

import_mtxzip(
  .data,
  path,
  ...,
  exdir = tempfile(),
  overwrite = FALSE,
  verbose = FALSE
)

Arguments

.data

(optional) When present, a data.frame or derived class, e.g., tibble, containing a single row, and a column specified by the 'path' argument and containing a path to a remote ('http://' or 'https://') or local '.zip' archive.

'.data' can also be a 'character(1)' argument used to provide the path to the '.zip' archive directly.

path

character(1) the path to the remote ('http://' or 'https://') or local '.zip' archive or, when '.data' is present, the column name (default '"path"') in which the path is found.

...

additional arguments, not supported.

verbose

logical(1) report progress using 'message()'.

exdir

character(1) directory in which to extract .zip archive.

overwrite

logical(1) overwrite existing files in 'exdir'?

Value

'SingleCellExperiment()' representing the expreession data. Rows represent features and columns cells; counts are represented in a sparse matrix.

Examples

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## Not run: 
loom <-
    available("loom") 
    filter(size == min(size)) 
    import_loom()

## End(Not run)
## Not run: 
mtx <-
    available("mtx.zip") 
    filter(size == min(size)) 
    import_mtxzip()

## End(Not run)

mtmorgan/HCAmtxzip documentation built on Nov. 24, 2019, 12:26 p.m.