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PNAAssay5 Methods

PNAAssay5-methods.Rd

Methods for PNAAssay5 objects for generics defined in other packages

Join Layers Together

Usage

# S3 method for class 'PNAAssay5'
RenameCells(object, new.names = NULL, ...)

# S4 method for class 'PNAAssay5'
show(object)

# S3 method for class 'PNAAssay5'
subset(x, features = NULL, cells = NULL, ...)

# S3 method for class 'PNAAssay5'
merge(
  x = NULL,
  y = NULL,
  merge.data = TRUE,
  add.cell.ids = NULL,
  collapse = TRUE,
  ...
)

# S3 method for class 'PNAAssay5'
JoinLayers(object, layers = NULL, new = NULL, ...)

Arguments

object

A PNAAssay5 object.

new.names

A character vector with new cell IDs. The length of the vector must be equal to the number of cells in the object and the names must be unique.

...

Additional arguments passed to other methods

x

A PNAAssay5 object

features

Feature names

cells

Cell names

y

A PNAAssay5 object or a list of PNAAssay5 objects

merge.data

Merge the data slots instead of just merging the counts (which requires renormalization); this is recommended if the same normalization approach was applied to all objects

add.cell.ids

A character vector with sample names

collapse

If TRUE, merge layers of the same name together

layers

A character vector of layer names to join.

new

Name of new layers

Value

A PNAAssay5 object with layers joined

Functions

  • RenameCells(PNAAssay5): Rename cell IDs of a PNAAssay5 object

  • show(PNAAssay5): Show method for PNAAssay5 objects

  • subset(PNAAssay5): Subset a PNAAssay5 object

  • merge(PNAAssay5): Merge two or more PNAAssay5 objects together

  • JoinLayers(PNAAssay5): Join layers

Examples

library(SeuratObject)
options(Seurat.object.assay.version = "v5")
# Load example data as a Seurat object
pxl_file <- minimal_pna_pxl_file()
seur_obj <- ReadPNA_Seurat(pxl_file)
#> ✔ Created a <Seurat> object with 5 cells and 158 targeted surface proteins

# Merge Seurat objects
seur_obj_merged <- merge(seur_obj, seur_obj)
#> Warning: Some cell names are duplicated across objects provided. Renaming to enforce unique cell names.
pna_assay <- seur_obj_merged[["PNA"]]

# The PNAAssay5 now has two count matrices
pna_assay
#> PNAAssay (v5) data with 158 features for 10 cells
#> Top 10 variable features:
#>  HLA-ABC, B2M, CD11b, CD11c, CD18, CD82, CD8, TCRab, HLA-DR, CD45 
#> Layers:
#>  counts.1, counts.2 
#> Loaded CellGraph objects:
#>  0

# Join layers
pna_assay <- JoinLayers(pna_assay)

# Now the PNAAssay5 has a single, merged count matrix
pna_assay
#> PNAAssay (v5) data with 158 features for 10 cells
#> Top 10 variable features:
#>  HLA-ABC, B2M, CD11b, CD11c, CD18, CD82, CD8, TCRab, HLA-DR, CD45 
#> Layers:
#>  counts 
#> Loaded CellGraph objects:
#>  0

# JoinLayers now also works on the Seurat object directly
seur_obj_merged <- JoinLayers(seur_obj_merged)
seur_obj_merged[["PNA"]]
#> PNAAssay (v5) data with 158 features for 10 cells
#> Top 10 variable features:
#>  HLA-ABC, B2M, CD11b, CD11c, CD18, CD82, CD8, TCRab, HLA-DR, CD45 
#> Layers:
#>  counts 
#> Loaded CellGraph objects:
#>  0