Read a count matrix from a pxl file

Usage

ReadMPX_counts(filename, return_list = FALSE, verbose = TRUE)

Arguments

filename: Path to a .pxl file
return_list: If TRUE, returns a list with the expression matrix and the output from h5read
verbose: Print messages

Value

A count matrix or a list if return_list = TRUE

Examples

library(pixelatorR)

# Load example data
pxl_file <- system.file("extdata/five_cells",
  "five_cells.pxl",
  package = "pixelatorR"
)
counts <- ReadMPX_counts(pxl_file)
#> ℹ Loading count data from /private/var/folders/gw/bdcqhnvs0m9gs_mq8n51jtbc0000gn/T/Rtmpn9YTAb/temp_libpath1398336799173/pixelatorR/extdata/five_cells/five_cells.pxl
counts[1:5, 1:5]
#>       RCVCMP0000217 RCVCMP0000118 RCVCMP0000487 RCVCMP0000655 RCVCMP0000263
#> CD274            18             6             9            23            22
#> CD44            117            49           100           338           417
#> CD25             14             5            13             9            34
#> CD279            39             1             7             8             2
#> CD41              2            18            18             9             2