process_input: process input data from ST pipeline to make sure they conform...
In tmirus/TTT: What the Package Does (One Line, Title Case)

process input data from ST pipeline to make sure they conform to the format the package expects

process_input(
  counts,
  ids = NULL,
  img_path = NULL,
  separate_by = "x",
  force_counts = FALSE,
  force_indices = FALSE,
  dup.sep = "_",
  n.gene.cutoff = 100,
  verbose = TRUE,
  normalize = FALSE
)

`counts`	non-negative numeric matrix containing gene counts, rows correspond to spots, columns correspond to genes
`ids`	data frame or matrix assigning spatial coordinates to the spots, the spot 0,0 is in the right lower corner of the corresponding tissue slide and the number of spots along the X-axis is higher than the number of spots on the Y-axis. optional if spatial information is contained in rownames of counts
`img_path`	character, optional. file path to ST slide image
`separate_by`	only necessary if spatial information is given as in the output of ST Pipeline (Navarro et al.), e.g. 32x2; default x
`force_counts`	logical, in case there are less genes than spots this needs to be TRUE; default FALSE
`force_indices`	logical, in case the range of x and y indices is not the same as in the ST barcode files
`dup.sep`	character, optional; if duplicate gene names are distinguished by e.g. 1, 2 at the end, pass dup.sep="" to try to combine these columns; default ""
`n.gene.cutoff`	integer > 0, number of genes that need to be expressed in a spots in order for the spot not to be removed from the data
`verbose`	logical, default TRUE
`normalize`	logical, default FALSE