Append data from an h5Seurat file to a preexisting Seurat object

AppendData(
  file,
  object,
  assays = NULL,
  reductions = NULL,
  graphs = NULL,
  images = NULL,
  extras = "commands",
  overwrite = FALSE,
  verbose = TRUE,
  ...
)

# S3 method for character
AppendData(
  file,
  object,
  assays = NULL,
  reductions = NULL,
  graphs = NULL,
  images = NULL,
  extras = "commands",
  overwrite = FALSE,
  verbose = TRUE,
  ...
)

# S3 method for H5File
AppendData(
  file,
  object,
  assays = NULL,
  reductions = NULL,
  graphs = NULL,
  images = NULL,
  extras = "commands",
  overwrite = FALSE,
  verbose = TRUE,
  ...
)

# S3 method for h5Seurat
AppendData(
  file,
  object,
  assays = NULL,
  reductions = NULL,
  graphs = NULL,
  images = NULL,
  extras = "commands",
  overwrite = FALSE,
  verbose = TRUE,
  ...
)

Arguments

file

Name of h5Seurat or connected h5Seurat file to load

object

A Seurat object to append data to

assays

One of:

  • A character vector with names of assays

  • A character vector with one or more of counts, data, scale.data describing which slots of all assays to load

  • A named list where each entry is either the name of an assay or a vector describing which slots (described above) to take from which assay

  • NULL for all assays

  • FALSE for no assays

reductions

One of:

  • A character vector with names of reductions

  • NULL for all reductions

  • NA for global reductions

  • FALSE for no reductions

Note: Only reductions associated with an assay loaded in assays or marked as global will be loaded

graphs

One of:

  • A character vector with names of graphs

  • NULL for all graphs

  • FALSE for no graphs

Note: Only graphs associated with an assay loaded in assays will be loaded

images

One of:

  • A character vector with names of images

  • NULL for all images

  • NA for global images

  • FALSE for no images

extras

Extra information to load; supports any combination of the following values:

“commands”

Load command logs. If overwrite = TRUE, replaces existing command logs

overwrite

Overwrite existing data in object with data from file

verbose

Show progress updates

...

Arguments passed to other methods

Value

object with the extra data requested