The main user-facing function to download annotations and ion images for a METASPACE dataset.
Usage
get_metaspace(
dataset_id,
fdr = 0.1,
database = c("HMDB", "v4"),
include_images = TRUE,
api_key = NULL,
isotope_idx = 1,
relative = 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")).
- include_images
Logical, if TRUE, downloads all ion image matrices (default = TRUE).
- api_key
Optional character string, your METASPACE API key (default = NULL).
- isotope_idx
Integer, index of the isotope image to download for all annotations (1 for main peak) (default = 1).
- relative
Logical, if TRUE, normalizes pixel intensities (0-1 range) (default = TRUE).
Examples
utils::str(formals(get_metaspace))
#> Dotted pair list of 7
#> $ dataset_id : symbol
#> $ fdr : num 0.1
#> $ database : language c("HMDB", "v4")
#> $ include_images: logi TRUE
#> $ api_key : NULL
#> $ isotope_idx : num 1
#> $ relative : logi TRUE
# get_metaspace(dataset_id = "2020-12-07_03h16m14s", fdr = 0.1, database= c("HMDB", "v4"), relative = TRUE)