Adds metabolite annotations to respective m/z values generated using an FMP10 matrix. This is done based on a curated FMP10 matrix database.
Usage
AddFMP10Annotations(
obj,
only.fmp.adduct = FALSE,
add.custom.annotation = NULL,
assay = "Spatial",
return.only.annotated = FALSE,
mass.threshold = 0.05,
annotation.column = "all_IsomerNames",
database = NULL,
database_version = "latest",
database_source = c("auto", "bundled", "local"),
database_local_dir = NULL
)Arguments
- obj
SpaMTP Seurat object containing m/z intensity values for annotation. Data should be generated with a FMP10 matrix.
- only.fmp.adduct
Boolean indicating if only metabolites with FMP10+ adducts (
+FMP10, +2FMP10, etc.) should be assigned to m/z values (default = FALSE).- add.custom.annotation
data.frame containing addition FMP10 metabolite annotations that are not in the current FMP10 database. Note: this data.frame must contain these column c("mass", "annotation", "Adduct", "Formula", "Isomers", "Isomers_IDs"). If set to NULL, only reference FMP10 database will be used (default = NULL).
- assay
Character string defining the Seurat object assay to store the respective annotations in the feature meta.data dataframe (default = "Spatial").
- return.only.annotated
Boolean defining whether to return a SpaMTP Seurat object containing only successfully annotated m/z values (default = FALSE).
- mass.threshold
Numeric value defining the acceptable threshold (plus-minus) between the custom annotations and the actual m/z values contained within the SpaMTP object (default = 0.05).
- annotation.column
Character string defining the feature meta.data column name that will contain the assigned annotations (default = "all_IsomerNames").
- database
Optional named list of database resources, normally created by
LoadSpaMTPDatabase().- database_version
Database snapshot version used for annotation lookup.
- database_source
Database source; see
LoadSpaMTPDatabase().- database_local_dir
Optional local RDS resource directory.
Value
SpaMTP Seurat object containing the relative metabolite annotations stored in the feature metadata dataframe.
Examples
utils::str(formals(AddFMP10Annotations))
#> Dotted pair list of 11
#> $ obj : symbol
#> $ only.fmp.adduct : logi FALSE
#> $ add.custom.annotation: NULL
#> $ assay : chr "Spatial"
#> $ return.only.annotated: logi FALSE
#> $ mass.threshold : num 0.05
#> $ annotation.column : chr "all_IsomerNames"
#> $ database : NULL
#> $ database_version : chr "latest"
#> $ database_source : language c("auto", "bundled", "local")
#> $ database_local_dir : NULL
# AddFMP10Annotations(spamtp, only.fmp.adduct = FALSE)