find_Background: Finds background components in Peak.list

In USEPA/LUMA: LCMS-Based Untargeted Metabolomics Assistant

Description

Find components within Peak.list that are also present in the process blanks below a user-defined sample:blank ratio. See remove_background_peaks and CullBackground for examples that use this function.

Usage

find_Background(
  object,
  Peak.list,
  Solv.list,
  Sample.df,
  search.par,
  lib_db,
  ion.id,
  QC.id,
  MB.id,
  db.id,
  ion.mode
)

## S3 method for class 'mz'
find_Background(
  object,
  Peak.list,
  Solv.list,
  Sample.df,
  search.par,
  lib_db,
  ion.id,
  QC.id,
  MB.id,
  db.id,
  ion.mode
)

## S3 method for class 'monoMass'
find_Background(
  object,
  Peak.list,
  Solv.list,
  Sample.df,
  search.par,
  lib_db,
  ion.id,
  QC.id,
  MB.id,
  db.id,
  ion.mode
)

Arguments

object	used for method dispatch. Can be any object. See usage for details
Peak.list	data table containing sample data
Solv.list	data table containing blank data
Sample.df	a data frame with class info as columns. Must contain a separate row entry for each unique sex/class combination. Must contain the columns 'Sex','Class','n','Endogenous'.
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".
lib_db	RSQLite connection
ion.id	character vector specifying identifier in filename designating positive or negative ionization mode or both. Positive identifier must come first. Default is c('Pos','Neg')
QC.id	character vector specifying identifier in filename designating a Pooled QC sample. Only the first value will be used. Default is 'Pooled_QC_'
MB.id	character vector specifying identifier in filename designating a Method Blank. Only the first value will be used. Default is '^MB'
db.id	character vector specifying identifiers in database names designating sample \[1\] and blank \[2\] databases. Default is c('Peaklist','Blanks')
ion.mode	a character vector defining the ionization mode. Must be either 'Positive', 'Negative' or both. Default is c('Positive','Negative')

Value

nested list a list for each ionization mode, each containing a list of two dataframes: the first contains the intensity matrix for the peaklist with solvent peaks removed, the second contains the intensity matrix for the solvent peaks

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