filter_advise_lipidomics: filter_advise_lipidomics

In ShinyFabio/ADViSELipidomics: Shinyapp for the acquisition and the analysis of lipidomics data

filter_advise_lipidomics

Description

filter_advise_lipidomics is the function for filtering lipid data on several features.

Usage

filter_advise_lipidomics(
  out,
  ca_bound = c(14, 24),
  db_bound = c(0, 6),
  data_type = "LipidSearch"
)

Arguments

out	List. It is the result from the read_advise_lipidomics function.
ca_bound	Numerical vector. It is the range of the carbon atoms for each lipid species: first number is the lower bound, second number is the upper bound. Default = c(14,24).
db_bound	Numerical vector. It is the range of the double bonds for each lipid species: first number is the lower bound, second number is the upper bound. Default = c(0,6).
data_type	Character. Where come from the data. Can be "LipidSearch" or "LIQUID".

Details

The filter step is composed of different filters applied on non-labeled files: a) retention time, the retention times of the lipid species should be in the range reported in the internal standard file for each class; b) carbon atom, the carbon atoms of the lipid species should be in the range reported in the internal standard file for each class, and should be an even number; c) double bond, the double bonds of the lipid species should be in the range reported in the internal standard file for each class; d) duplicated area, the duplicated areas for a lipid species should be ingnored, conserving only the minimum area for one lipid species (duplication is checkd on m/z values). After this step, filtered data are stored separately from raw data.

Value

res: a list with results from the reading step, updated with the filtered data, divided into non-labeled data (lipid_filtered) and deuterated data (lipid_deuterated).

Note

Last change 17/12/2021

ShinyFabio/ADViSELipidomics documentation built on March 21, 2023, 7:30 a.m.