parse_neg_results: CAMERA Parser in negative mode

In USEPA/LUMA: LCMS-Based Untargeted Metabolomics Assistant

Description

Parses the CAMERA results using well-defined rules to eliminate conflicting annotations.

Usage

parse_neg_results(raw, rule, IonMode)

Arguments

raw	a data frame with variables as columns. Should contain all output columns from XCMS and CAMERA, additional columns from match_Annotation and calc_minfrac. Must contain the CAMERA columns "isotopes","adduct","pcgroup".
rule	a data frame containing the rule list used by CAMERA to annotate ion adducts and fragments. Must contain the columns "name","nmol","charge","massdiff","oidscore", "quasi","ips".
IonMode	a character string defining the ionization mode. Must be "Negative"

Value

data frame parsed version of the original data frame with additional columns "mono_mass","metabolite_group","monoisotopic_flg", "adduct_flg","isotope_flg","ambiguity_flg","Selection_flg".

Examples

library(LUMA)
if(require(lcmsfishdata, quietly = TRUE)) {

  file <- system.file("extdata","primary_adducts_neg.csv", package =
  "lcmsfishdata") # is case sensitive on Linux
  rules <- read.csv(file, header = TRUE)
  Peak.list <- as.data.frame(lcmsfishdata::Peaklist_Neg[["Annotated"]])
  test <- parse_neg_results(raw = Peak.list, rule = rules, IonMode = "Negative")
  colnames(test)[-which(colnames(test) %in% colnames(Peak.list))] ##Adds the following columns
  length(unique(Peak.list[["pcgroup"]])) #Originally were this many metabolite groupings
  length(unique(test[["metabolite_group"]])) #Now there are many more metabolite groupings

}

USEPA/LUMA documentation built on Aug. 29, 2020, 1:40 p.m.