assessPuritySingle {msPurity}R 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)

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)

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)

[Package msPurity version 1.6.2 Index]