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SeuratObject 5.0.0
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@mojaveazure mojaveazure released this 27 Oct 21:45
· 83 commits to master since this release
v5.0.0
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Added

  • New Assay5 class with support for layers; layers provide support for:
    • arbitrary expression matrix names and number
    • arbitrary expression matrix shape
    • disk-backed expression matrices
  • New $ method for Assay and Assay5 objects to pull expression matrices, replacing informal usage of @
  • New LayerData() and LayerData()<- functions to replace GetAssayData() and SetAssayData(), respectively
  • Support for renaming cells and features with dimnames()<- (changing feature names does not apply to v3 Assay objects)
  • New SaveSeuratRds() and LoadSeuratRds() to save and load Seurat objects with disk-backed layers
  • New droplevels.LogMap() to drop unused entries from a LogMap
  • New ability to split (split()) and rejoin layers (JoinLayers()) within Assay and Assay5 objects based on grouping factor

Changes

  • slot argument deprecated in all contexts; where applicable, replaced with layer argument
  • [ for Assay and Assay5 objects take a layer name to pull an expression matrix
    • option Seurat.object.assay.brackets allows restoring v3/v4 behavior of subsetting the main expression matrix (eg. data)
  • Stricter object validation routines at all levels
  • PackageCheck() deprecated in favor of rlang::check_installed()
  • AttachDeps() deprecated in favor of using the Depends field of DESCRIPTION
  • Subobjects within a Seurat object may have subsets of cells present at the object level
  • Begun replacement of stop() and warning() with rlang::abort() and rlang::warn() for easier debugging
  • Expanded validation and utility of KeyMixin objects

Removed

  • Unused object constructors (eg. Assay(), Seurat())
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