Bin SpaMTP Object — BinSpaMTP • SpaMTP

Bins m/z peaks of a specified SpaMTP object to reduce dimensionality and remove noise.

Usage

BinSpaMTP(
  data,
  resolution,
  units = "ppm",
  assay = "Spatial",
  slot = "counts",
  method = c("sum"),
  return.only.mtx = FALSE
)

Arguments

data: SpaMTP Seurat Object containing the intensity data to be binned
resolution: Numeric value indicating the relative bin size to use when binning the intensity data.
units: Character string defining the relative units of the provided resolution size. Values can be either 'ppm' or 'mz' (default = 'ppm').
assay: Character string defining the SpaMTP assay to extract intensity values from (default = "Spatial").
slot: Character string defining the assay slot containing the intensity values (default = "counts").
method: A character vector specifying the binning method. Input values must be either "sum", "mean", "max" or "min" (default = "sum").
return.only.mtx: Boolean value indicating whether to return only the binned intensity matrix. If FALSE, a SpaMTP object will be returned with the binned values stored in an assay called binned (default = FALSE).

Value

Either a binned intensity matrix or a SpaMTP object contatining the binned intensity matrix stored in the binned assay.

Examples

utils::str(formals(BinSpaMTP))
#> Dotted pair list of 7
#>  $ data           : symbol 
#>  $ resolution     : symbol 
#>  $ units          : chr "ppm"
#>  $ assay          : chr "Spatial"
#>  $ slot           : chr "counts"
#>  $ method         : language c("sum")
#>  $ return.only.mtx: logi FALSE
#BinSpaMTP(spamtp.obj, resolution = 10, units = "ppm", return.only.mtx = TRUE)