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,
      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)

[Package msPurity version 1.16.2 Index]