Load the Proximity scores table from a PNA PXL file

Load the Proximity scores table from a PNA PXL file

Usage

ReadPNA_proximity(
  pxl_file,
  calc_log2_ratio = TRUE,
  lazy = FALSE,
  verbose = TRUE
)

Arguments

pxl_file

Path to a PXL file containing PNA data

calc_log2_ratio

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

lazy

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

verbose

Print messages

Value

A tbl_df or a tbl_lazy with PNA Proximity scores

See also

Other data-loaders: ReadMPX_Seurat(), ReadMPX_item()

Examples

library(pixelatorR)

pxl_file <- minimal_pna_pxl_file()
proximity_tbl <- ReadPNA_proximity(pxl_file)
#> ℹ Loading proximity scores from: /home/ubuntu/R/library/pixelatorR/extdata/five_cells/minimal_PNA_PBMC.pxl
#> duckdb keeps downloaded extensions and secrets in a temporary directory:
#> ℹ /tmp/Rtmp3BjCtL/duckdb
#> This is removed when the R session ends.
#> • Extensions are re-downloaded each session.
#> • Secrets are lost.
#> ℹ Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
#> ℹ Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
#> ℹ See ?duckdb_storage for details and alternatives.
#> ✔ Returning a <tbl_df> with the PNA proximity scores
proximity_tbl
#> # A tibble: 58,696 × 9
#>    marker_1 marker_2 join_count join_count_expected_mean join_count_expected_sd
#>    <chr>    <chr>         <dbl>                    <dbl>                  <dbl>
#>  1 CD56     CD56              0                     0                     0    
#>  2 CD56     mIgG2b            0                     0.03                  0.171
#>  3 CD56     CD71              0                     0.01                  0.1  
#>  4 CD56     CD6               0                     2.07                  1.58 
#>  5 CD56     Siglec-9          0                     0.03                  0.171
#>  6 CD56     CD79a             0                     0                     0    
#>  7 CD56     NKp80             0                     0                     0    
#>  8 CD56     CD85j             0                     0.17                  0.378
#>  9 CD56     IgM               0                     0.08                  0.307
#> 10 CD56     TCRva7.2          0                     0.01                  0.1  
#> # ℹ 58,686 more rows
#> # ℹ 4 more variables: join_count_z <dbl>, join_count_p <dbl>, component <chr>,
#> #   log2_ratio <dbl>