Convert objects to a PNAAssay5

Convert objects to a PNAAssay5

Usage

as.PNAAssay5(x, ...)

# S3 method for class 'Assay5'
as.PNAAssay5(x, cellgraphs = NULL, proximity = NULL, fs_map = NULL, ...)

Arguments

x

An object to convert to class PNAAssay5

...

Arguments passed to other methods

cellgraphs

A list of CellGraph objects

proximity

A tbl_df with proximity scores

fs_map

A tbl_df with information on source PXL file paths, sample IDs, and component IDs

Value

A PNAAssay5 object

Examples

library(pixelatorR)
library(dplyr)
library(SeuratObject)

pxl_file <- minimal_pna_pxl_file()
counts <- ReadPNA_counts(pxl_file)
assay <- CreateAssay5Object(
  counts = counts
)
pna_assay5 <- as.PNAAssay5(
  assay,
  cellgraphs = rep(list(NULL), ncol(counts)) %>%
    setNames(colnames(counts))
)
pna_assay5
#> PNAAssay (v5) data with 158 features for 5 cells
#> First 10 features:
#>  HLA-ABC, B2M, CD11b, CD11c, CD18, CD82, CD8, TCRab, HLA-DR, CD45 
#> Layers:
#>  counts 
#> Loaded CellGraph objects:
#>  0