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Load data from PNA PXL file into a Seurat object

ReadPNA_Seurat.Rd

This function can be used to load data from a PXL file, and returns a Seurat object.

Usage

ReadPNA_Seurat(
  pxl_file,
  assay = "PNA",
  return_pna_assay = TRUE,
  load_proximity_scores = TRUE,
  calc_log2_ratio = TRUE,
  verbose = TRUE,
  ...
)

Arguments

pxl_file

Path to a PXL file

assay

Assay name

return_pna_assay

Logical specifying whether the count data should be stored in a PNAAssay/PNAAssay5. If set to FALSE, the count data will be stored in a Assay/Assay5 instead. For the latter case, many features provided in pixelatorR will be unavailable. This can be useful if you only intend to analyze the abundance data.

load_proximity_scores

Logical specifying whether the proximity scores should be loaded into the PNAAssay/PNAAssay5. If you only intend to analyze abundance data or PNA graphs, you can set this parameter to FALSE to use less memory. This parameter only have an effect if return_pna_assay = TRUE.

calc_log2_ratio

A logical specifying whether to calculate and add a log2ratio column to the output table. Default is TRUE

verbose

Print messages

...

Additional parameters passed to CreateSeuratObject

Value

An object of class Seurat

Details

By default, the count matrix is returned in a PNAAssay object. If the global option Seurat.object.assay.version is set to "v5", the function will return a PNAAssay5 object instead.

See also

Other PXL-data-loaders: ReadPNA_counts(), ReadPNA_metadata()

Examples

library(pixelatorR)

# Crete example 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
seur_obj
#> An object of class Seurat 
#> 158 features across 5 samples within 1 assay 
#> Active assay: PNA (158 features, 158 variable features)
#>  1 layer present: counts