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Load the edge list from a PNA PXL file

ReadPNA_edgelist.Rd

Note that the umi1 and umi2 sequences are encoded as integer64 which is not natively supported by R. The bit64 package is required to read these IDs and conversion to integer or numeric should be avoided. It is safer to convert these to character vectors if needed for downstream processing.

Usage

ReadPNA_edgelist(
  pxl_file,
  cells = NULL,
  umi_data_type = c("int64", "string", "suffixed_string"),
  lazy = TRUE
)

Arguments

pxl_file

Path to a PXL file with a PNA data set

cells

A character vector with component IDs. If NULL, all components are loaded.

umi_data_type

One of "int64", "string" or "suffixed_string". Default is "int64".

  • "int64": The UMIs are encoded as int64

  • "string": The UMIs are encoded as character

  • "suffixed_string": The UMIs are encoded as character with a suffix '-umi1' or '-umi2' added

lazy

A logical specifying whether to load the data lazily. If TRUE, a tbl_lazy object is returned.

Value

A tbl_df or, if lazy = TRUE, a tbl_lazy object with the edge list:

  • marker_1: The first protein

  • marker_2: The second protein

  • umi1: A unique ID of the first RCA product

  • umi2: A unique ID of the second RCA product

  • read_count: The number of reads supporting the edge

  • uei_count: The number of unique event identifiers (UEIs) supporting the edge. This column is optional and is only returned if it is present in the edgelist table.

  • component: The component name