S4 class for assignment parameters
AssignmentParameters-class.Rd
An S4 class to store assignment parameters.
Slots
technique
the analytical technique
correlations_parameters
a list of correlation parameters to be passed to
metabolyseR::correlations()
max_M
the maximum molecular mass for which to assign molecular formulas
MF_rank_threshold
rank threshold for molecular formula selection
ppm
the parts per million error threshold
limit
the atomic mass unit deviation limit for relationship calculation
RT_diff_limit
the limit for retention time differences for correlated features in adduct and isotopic assignment
adducts
a list of character vectors containing the adducts names. List element names should denote ionisation mode. The order that these adducts are provided denotes their expected relative importance to assignments with the first expected to be the most common and the last the least common within each ionisation mode.
isotopes
a character vector of isotopes to use. Similarly to the adducts, their order denotes the expected commonality in the data.
transformations
a character vector of transformations molecular formula changes
adduct_rules
a tibble containing the adduct formation rules as returned by
mzAnnotation::adduct_rules()
isotope_rules
a tibble containing the isotope rules as returned by
mzAnnotation::isotope_rules()
transformation_rules
tibble containing the transformation rules as returned by
mzAnnotation::transformation_rules()