remove_void_volume: Removes void volume from Peak.list

In USEPA/LUMA: LCMS-Based Untargeted Metabolomics Assistant

Description

Removes features or compounds found in the void volume of the chromatographic run from the Peak.list

Usage

remove_void_volume(Peak.list, search.par, method, ...)

Arguments

Peak.list	data frame. Must have Correlation.stat column. Should contain output columns from XCMS and CAMERA, and additional columns from IHL.search, Calc.MinFrac, Calc.corr.stat and EIC.plotter functions.
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".
method	which method to apply to trim by retention time. See trim_rt() for details.
...	Arguments to pass to trim_rt().

Value

data frame Peak.list.trimmed original Peak.list without all metabolite groups containing at least one feature in the void volume

Examples

library(LUMA)
if(require(lcmsfishdata, quietly = TRUE)){
# is case sensitive on Linux
file <- system.file('extdata','Search_Parameters.txt', package = "LUMA")
search.par <- read.table(file, sep = "\t", header = TRUE)
test <- remove_void_volume(Peak.list = lcmsfishdata::Peaklist_Pos$From_CAMERA, search.par =
search.par, method = "mz")

#Removes 275 features within the void volume
nrow(lcmsfishdata::Peaklist_Pos$From_CAMERA) - nrow(test)
}

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