This function loads raw spatial metabolic data in a .imzML and .ibd format and generates a SpaMTP Seurat Object.
This function adapts the readImzML function implmented in Cardinal to correctly import large data.
Usage
LoadSM(
name,
path,
mass.range = NULL,
resolution = 10,
units = "ppm",
verbose = TRUE,
assay = "Spatial",
bin_package = "SpaMTP",
multi.run = FALSE,
...
)Arguments
- name
Character string of the object name. This should match the filename.
- path
Character string defining the directory path of the file. This should not include the file name.
- mass.range
Vector of numeric values indicating the mass range to use for the imported data (default = NULL).
- resolution
Numeric value defining the the accuracy to which the m/z values will be binned after reading. This value can be in either "ppm" or "mz" depending on the units type specified (default = 10).
- units
Character string defining the resolution value unit type, either c("ppm", "mz") (default = "ppm")
- verbose
Boolean indicating whether to show informative processing messages. If TRUE the message will be show, else the message will be suppressed (default = TRUE)
- assay
Character string describing the name of the new assay which stores the imported data (default = "Spatial").
- bin_package
Character string defining the package used to bin the imported data. Options are either "SpaMTP" or "Cardinal" (default = "SpaMTP").
- multi.run
Boolean indicating if there are multiple runs within the imported data. If
TRUE, an index will be added to the pixel names per run, and an individual FOV will be generated per run in the Seurat Object (default = FALSE).- ...
Additional arguments passed to the
readMSIDatafunction.