purityX {msPurity} | R Documentation

## Assessing anticipated purity of XCMS features from an LC-MS run

### Description

Constructor for the purityX class.

Given an XCMS object get the anticipated precursor purity of the grouped peaks

### Usage

    purityX(
      xset,
      purityType = "purityFWHMmedian",
      offsets = c(0.5, 0.5),
      fileignore = NULL,
      cores = 1,
      xgroups = NULL,
      iwNorm = FALSE,
      iwNormFun = NULL,
      ilim = 0.05,
      plotP = FALSE,
      mzRback = "pwiz",
      isotopes = FALSE,
      im = NULL,
      singleFile = 0,
      rtrawColumns = FALSE,
      saveEIC = FALSE,
      sqlitePth = NULL
    )

### Arguments

`xset` | object; xcms object
`purityType` | character; Area and average used for the purity predictions. Options are "purityFWHMmedian", "purityFWmedian", "purityFWHMmean", "purityFWmean"
`offsets` | vector; vector of the isolation window upper and lower offsets
`fileignore` | vector; vector of files to ignore for the prediction calculation
`cores` | numeric; number of cores to use
`xgroups` | vector; vector of xcms groups to perform prediction on
`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)
`plotP` | boolean; TRUE if plot of the EIC of feature and associated contamination is the be save to the working directory
`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)
`singleFile` | numeric; If just a single file for purity is to be calculated (rather than the grouped XCMS peaks). Uses the index of the files in xcmsSet object. If zero this is ignored.
`rtrawColumns` | boolean; TRUE if the rt_raw values are included as additional columns in the @peaks slot (only required if using the obiwarp)
`saveEIC` | boolean; If True extracted ion chromatograms will be saved to SQLite database
`sqlitePth` | character; If saveEIC True, then a path to sqlite database can be used. If NULL then a database will be created in the working directory called eics

### Value

a purityX object containing a dataframe of predicted purity scores

### Examples

    msPths <- list.files(system.file("extdata", "lcms", "mzML",
                        package="msPurityData"), full.names = TRUE,
                        pattern = "LCMS_")
    xset <- xcms::xcmsSet(msPths)
    xset <- xcms::group(xset)
    xset <- xcms::retcor(xset)
    xset <- xcms::group(xset)
    ppLCMS <- purityX(xset, cores = 1, xgroups = c(1, 2))

[Package msPurity version 1.14.1 Index]