dimsPredictPuritySingle {msPurity} | R Documentation

## Predict the precursor purity from a DI-MS dataset

### Description

Given a an DI-MS dataset (either mzML or .csv file) calculate the predicted purity for a vector of mz values.

Calculated at a given offset e.g. for 0.5 +/- Da the minOffset would be 0.5 and the maxOffset of 0.5.

A ppm tolerance is used to find the target mz value in each scan.

### Usage

    dimsPredictPuritySingle(
      mztargets,
      filepth,
      minOffset = 0.5,
      maxOffset = 0.5,
      ppm = 2.5,
      mzML = TRUE,
      iwNorm = FALSE,
      iwNormFun = NULL,
      ilim = 0.05,
      mzRback = "pwiz",
      isotopes = TRUE,
      im = NULL,
      sim = FALSE
    )

### Arguments

`mztargets` | vector = mz targets to get predicted purity for
`filepth` | character = mzML file path or .csv file path
`minOffset` | numeric = isolation window minimum offset
`maxOffset` | numeric = isolation window maximum offset
`ppm` | numeric = tolerance for target mz value in each scan
`mzML` | boolean = Whether an mzML file is to be used or .csv file (TRUE == mzML)
`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)
`sim` | boolean = TRUE if file is from sim stitch experiment. Default FALSE

### Value

a dataframe of the target mz values and the predicted purity score

### Examples

    mzmlPth <- system.file("extdata", "dims", "mzML", "B02_Daph_TEST_pos.mzML",
                           package="msPurityData")
    predicted <- dimsPredictPuritySingle(c(173.0806, 216.1045), filepth=mzmlPth,
                                 minOffset=0.5, maxOffset=0.5, ppm=5, mzML=TRUE)

[Package msPurity version 1.14.1 Index]