construction | R Documentation |
Perform consensus structural classification for molecular formulas assigned to m/z features from electrospray ionisation mass spectrometry approaches.
construction(
x,
library_path = tempdir(),
db = "kegg",
organism = character(),
threshold = 66,
adduct_rules_table = adduct_rules(),
classyfireR_cache = NULL
)
## S4 method for signature 'tbl_df'
construction(
x,
library_path = paste0(tempdir(), "/construction_library"),
db = "kegg",
organism = character(),
threshold = 66,
adduct_rules_table = adduct_rules(),
classyfireR_cache = NULL
)
## S4 method for signature 'Assignment'
construction(
x,
library_path = tempdir(),
db = "kegg",
organism = character(),
threshold = 66,
classyfireR_cache = NULL
)
x |
The molecular formulas and adducts to search. This should either be a tibble containing two character columns named |
library_path |
the target file path for the classification library in which to store consensus classification data |
db |
the databases to search. This can either be |
organism |
the KEGG organism ID. This is Ignored if argument |
threshold |
the percentage majority threshold for consensus classification |
adduct_rules_table |
a data frame containing the adduct formation rules. The defaults is |
classyfireR_cache |
the file path for a |
If argument x
is a tibble, then a tibble is returned containing the consensus structural classifications. If argument x
is an object of S4 class Assignment
, and object of S4 class Construction
is returned.
x <- tibble::tibble(MF = c('C12H22O11','C4H6O5'),
Adduct = c('[M+Cl]1-','[M-H]1-'))
structural_classifications <- construction(x)
structural_classifications
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