ume (version 1.5.2)

filter_int: Filter by (relative) peak magnitude

Description

This function filters molecular formulas by (relative) peak abundances.

Usage

filter_int(mfd, norm_int_min = NULL, norm_int_max = NULL, verbose = FALSE, ...)

Value

data.table; subset of original molecular formula table

Arguments

mfd

data.table with molecular formula data as derived from ume::assign_formulas. Column names of elements/isotopes must match names in the isotope column of ume::masses; values are integers representing counts per formula.

norm_int_min

Lower threshold (>=) of (normalized) peak magnitude

norm_int_max

Upper threshold (<=) of (normalized) peak magnitude

verbose

logical; if TRUE, show progress messages.

...

Arguments passed on to calc_norm_int

ms_id

Character; name of the column identifying individual spectra (default: "file_id").

peak_id

Character; name of the column identifying unique peaks (default: "peak_id").

peak_magnitude

Character; name of the column containing peak intensity values (default: "i_magnitude").

normalization

Character; normalization method to apply. One of "bp", "sum", "sum_ubiq", "sum_rank", "none". Default is "bp".

n_rank

Integer; number of top-ranked peaks to use for "sum_rank" normalization (default: 200).

See Also

Other Formula subsetting: filter_mass_accuracy(), filter_mf_data(), remove_blanks(), subset_known_mf(), ume_assign_formulas(), ume_filter_formulas()

Examples

filter_int(mfd = calc_norm_int(mfd = mf_data_demo,
normalization = "sum_rank", n_rank = 100), norm_int_min = 1)