combine_ion_modes: Combines Peak.lists from Two Ionization Modes

In USEPA/LUMA: LCMS-Based Untargeted Metabolomics Assistant

Description

Combines the two single adduct ion mode feature tables into one for EIC plotting

Usage

combine_ion_modes(Peak.list, search.par, tbl.id, method, peak.db, ...)

Arguments

Peak.list	a named list of data frames (one per ionization mode) containing intensity matrices across all study samples and Pooled QCs. Names must be c("Positive","Negative"). Alternatively may use existing database connections by setting to NULL
search.par	a single-row data frame with 11 variables containing user-defined search parameters. Must contain the columns "ppm","rt","Voidrt","Corr.stat.pos","Corr.stat.neg", "CV","Minfrac", "Endogenous", "Solvent","gen.plots", "keep.singletons".
tbl.id	character vector of table names to draw from databases. First value should be table containing compounds from positive ionization, second should be table containing compounds from negative ionization. Default is NULL.
method	which method to apply to search for duplicate entries. See search_IonDup() for details.
peak.db	Formal class SQLiteConnection
...	Arguments to pass parameters to search_IonDup()

Value

data frame containing the intensity matrix for the peaklist with Duplicate IDs

Examples

library(LUMA)
if(require(lcmsfishdata, quietly = TRUE)) {
file <- system.file("extdata","Search_Parameters.txt", package =
"lcmsfishdata") # is case sensitive on Linux
search.par <- read.table(file, header = TRUE, sep = "\t")
class(method) <- method <- "monoMass"
Peak.list <- list(Positive =
    lcmsfishdata::Peaklist_db$Peaklist_Pos_Solvent_Peaks_Removed, Negative =
    lcmsfishdata::Peaklist_db$Peaklist_Neg_Solvent_Peaks_Removed)

test <- combine_ion_modes(Peak.list = Peak.list, search.par = search.par,
    method = method)

colnames(test)[-which(colnames(test) %in%
    colnames(Peak.list[["Positive"]]))] #Adds two new columns
length(which(duplicated(test[["Duplicate_ID"]]))) #number of ion mode
#duplicates found


class(method) <- method <- "mz"
Peak.list <- list(Positive = lcmsfishdata::Peaklist_Pos$output_parsed,
Negative = lcmsfishdata::Peaklist_Neg$output_parsed)
test <- combine_ion_modes(Peak.list = Peak.list, search.par = search.par,
method = method)
colnames(test)[-which(colnames(test) %in% colnames(Peak.list[["Positive"]]))]
#Adds two new columns
dupID.mz <- test[["Duplicate_ID"]][which(duplicated(test[["Duplicate_ID"]]))]
length(dupID.mz) #number of ion mode duplicates found
 
}

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