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

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

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 <- readRDS(system.file("extdata", "tests", "xcms", "ms_only_xset_OLD.rds", package="msPurity"))
xset@filepaths[1] <- msPths[basename(msPths)=="LCMS_1.mzML"]
xset@filepaths[2] <- msPths[basename(msPths)=="LCMS_2.mzML"]
px <- purityX(xset, singleFile = 1)

computational-metabolomics/msPurity documentation built on May 13, 2024, 7:36 p.m.