get_adducts_nl_links: Detect possible neutral losses, isotopes and adduct links.

In eMetaboHUB/MS-CleanR: Cleans MS Data for Easier Analyses

Detect possible neutral losses, isotopes and adduct links.

Description

Detect possible neutral losses, isotopes and adduct links.

Usage

get_adducts_nl_links(
  data_to_treat,
  samples_cols,
  threshold_rt,
  threshold_mz,
  detected_adducts,
  user_pos_neutral_refs = NA,
  user_neg_neutral_refs = NA,
  user_pos_adducts_refs = NA,
  user_neg_adducts_refs = NA
)

Arguments

data_to_treat	A data.frame containing peaks data.
samples_cols	A list of string containing the names of samples columns.
threshold_rt	A numerical value indicating the retention time tolerance.
threshold_mz	A numerical value indicating the mass tolerance in Dalton for the detection of adducts and neutral losses.
detected_adducts	A data.frame indicating which adducts were detected by MSDial.
user_neg_neutral_refs, user_pos_neutral_refs, user_pos_adducts_refs, user_neg_adducts_refs	An optional 2-column data.frame containing information about neutral losses, positive adducts or negative adducts (one column for the name and one column for the mass difference with the base compound). If no data.frame is provided, the package default list is used.

Value

A list of 3 data.frames: "links" containing detected links, "computed_massdiff" containing all pairs of positive/negative adducts pair mass differences and "filtered_massdiff" containing pairs of positive/negative adducts pair mass differences for adducts pair detected by MSDial.

eMetaboHUB/MS-CleanR documentation built on Jan. 3, 2024, 8:55 p.m.