Read a count matrix from a PXL file with PNA data

Read a count matrix from a PXL file with PNA data

Usage

ReadPNA_counts(pxl_file)

Arguments

pxl_file

Path to a PXL file

Value

A count matrix or a list if return_list = TRUE

See also

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

Examples

library(pixelatorR)

# Load example counts
pxl_file <- minimal_pna_pxl_file()
counts <- ReadPNA_counts(pxl_file)
#> 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.
counts[1:5, 1:5]
#> 5 x 5 sparse Matrix of class "dgCMatrix"
#>         0a45497c6bfbfb22 2708240b908e2eba c3c393e9a17c1981 d4074c845bb62800
#> HLA-ABC              865             2077             2480             2994
#> B2M                 1182             3448             5307             9753
#> CD11b                929               12               17                6
#> CD11c                133             1354               26                8
#> CD18                 716              780              326             1127
#>         efe0ed189cb499fc
#> HLA-ABC             2212
#> B2M                 6082
#> CD11b                  .
#> CD11c                  4
#> CD18                 523