purityX: Assessing anticipated purity of XCMS features from an LC-MS...

In msPurity: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics

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))

msPurity documentation built on Jan. 14, 2021, 2:44 a.m.