Downloads METASPACE data, converts it to a feature matrix, and packages it into a Seurat object with spatial metadata.
Usage
Load_METASPACE(
dataset_id,
fdr = 0.1,
database = c("HMDB", "v4"),
api_key = NULL,
relative = FALSE,
transform = FALSE,
verbose = TRUE
)Arguments
- dataset_id
Character string of the METASPACE dataset ID.
- fdr
Numeric, the FDR level threshold (default = 0.1).
- database
Character vector, specifying the database name and version (default = c("HMDB", "v4")).
- api_key
Optional character string, your METASPACE API key (default = NULL).
- relative
Logical, if TRUE, normalizes pixel intensities (0-1 range) (default = FALSE).
- transform
Boolean specifiying whether to transform/flip the image (default = FALSE).
- verbose
Boolean indicating whether to show the message. If TRUE the message will be show, else the message will be suppressed (default = TRUE).
Examples
utils::str(formals(Load_METASPACE))
#> Dotted pair list of 7
#> $ dataset_id: symbol
#> $ fdr : num 0.1
#> $ database : language c("HMDB", "v4")
#> $ api_key : NULL
#> $ relative : logi FALSE
#> $ transform : logi FALSE
#> $ verbose : logi TRUE
# Load_METASPACE(dataset_id = "2020-12-07_03h16m14s", fdr = 0.1, database= c("HMDB", "v4"), relative = TRUE)