assessPuritySingle: Assess the purity of a single LC-MS/MS or DI-MS/MS file

View source: R/purityA-constructor.R

assessPuritySingleR Documentation

Assess the purity of a single LC-MS/MS or DI-MS/MS file

Description

Given a filepath to an mzML file the precursor purity for any MS/MS scans will be outputed into a dataframe

Usage

assessPuritySingle(
  filepth,
  fileid = NA,
  mostIntense = FALSE,
  nearest = TRUE,
  offsets = NA,
  cores = 1,
  plotP = FALSE,
  plotdir = NULL,
  interpol = "linear",
  iwNorm = FALSE,
  iwNormFun = NULL,
  ilim = 0,
  mzRback = "pwiz",
  isotopes = TRUE,
  im = NULL,
  ppmInterp = 7
)

Arguments

filepth

character; mzML file path for MS/MS spectra

fileid

numeric; adds a fileid column (primarily for internal use for msPurity)

mostIntense

boolean; True if the most intense peak is used for calculation. False if the centered peak is used

nearest

boolean; True if the peak selected is as the nearest MS1 scan. If False then the preceding scan is used

offsets

vector; Overide the isolation offsets found in the mzML filee.g. c(0.5, 0.5)

cores

numeric; Number of cores to use

plotP

boolean; If TRUE a plot of the purity is to be saved

plotdir

vector; If plotP is TRUE plots will be saved to this directory

interpol

character; Type of interolation to be performed "linear", "spline" or "none"

iwNorm

boolean; If TRUE then the intensity of the isolation window will be normalised based on the iwNormFun function

iwNormFun

function; A function to normalise the isolation window intensity. The default function is very generalised and just accounts for edge effects

ilim

numeric; All peaks less than this percentage of the target peak will be removed from the purity calculation, default is 5% (0.05)

mzRback

character; Backend to use for mzR parsing

isotopes

boolean; TRUE if isotopes are to be removed

im

matrix; Isotope matrix, default removes C13 isotopes (single, double and triple bonds)

ppmInterp

numeric; Set the ppm tolerance for the precursor ion purity interpolation. i.e. the ppm tolerence between the precursor ion found in the neighbouring scans.

Value

a dataframe of the purity score of the ms/ms spectra

See Also

purityA

Examples

filepth <- system.file("extdata", "lcms", "mzML", "LCMSMS_1.mzML", package="msPurityData")

puritydf <- assessPuritySingle(filepth)

Viant-Metabolomics/msPurity documentation built on May 13, 2024, 8:23 a.m.