averageSpectraSingle: Calculates to average mz, intensity and signal-to-noise of...

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

Calculates to average mz, intensity and signal-to-noise of multiple scans from 1 MS datafile (mzML or .csv)

Description

Averages multiple scans of mass spectrometry data together. Each scan consisting of a minimum of intensity and mz values.

Works for either mzML or a .csv file consisting of mz, i, scanid, (optional: noise, backgroun, snr)

Signal-to-noise (SNR) can be calculated a number of ways. Default is to calculate the SN for every scan as the "Intensity of peak / the median intensity of the scan".

Alternatively if using a .csv file as input (and assigning the csvFile parameter to TRUE), a precalculated SNR can be one of the columns. The precalculated SNR can then be chosen by using the option 'precalc' for the parameter snMethod

The function will work for both LC-MS or DI-MS datasets.

Usage

averageSpectraSingle(
  filePth,
  rtscn = "all",
  scanRange = NA,
  timeRange = NA,
  clustType = "hc",
  ppm = 1.5,
  snthr = 3,
  cores = 1,
  av = "median",
  missingV = "ignore",
  minfrac = 0.6667,
  snMeth = "median",
  csvFile = FALSE,
  normTIC = FALSE,
  mzRback = "pwiz",
  MSFileReader = FALSE
)

Arguments

filePth	character; Path of the file to be processed
rtscn	character; Whether it is scans or retention time to be filtered. Use "all" if all scans to be used. ['rt', 'scns', 'all']
scanRange	vector; Scan range (if rtscn='scns') e.g. c(40, 69)
timeRange	vector; Time range (if rtscn='rt) e.g. c(10.3, 400.8) (only if using mzML file)
clustType	character; Type of clustering used either Hierarchical or just simple 1D grouping ['hc', 'simple']
ppm	numeric; The ppm error to cluster mz together
snthr	numeric; Signal to noise ratio threshold
cores	numeric; Number of cores used to perform Hierarchical clustering WARNING: memory intensive, default 2
av	character; What type of averaging to do between peaks
missingV	character; What to do with missing values (zero or ignore)
minfrac	numeric; Min fraction of scans with a grouped peak to be an accepted averaged peak
snMeth	character; Type of snMethod to use ['mean', 'median', 'precalc']. Precalc only applicable when using the csvFile parameter as TRUE
csvFile	boolean; A csv file can be used as input. Useful for thermo files where the MSFileReader API can extract peaklist. This can consist of an .csv file with the following columns c('mz', 'i', 'scanid', 'snr')
normTIC	boolean; If TRUE then RSD calculation will use the normalised intensity (intensity divided by TIC) if FALSE will use standard intensity
mzRback	character; Backend to use for mzR parsing
MSFileReader	boolean; Deprecapted. Use csvFile parameter

Value

dataframe of the median mz, intensity, signal-to-noise ratio.

Examples

mzmlPth <- system.file("extdata", "dims", "mzML", "B02_Daph_TEST_pos.mzML", package="msPurityData")
avP <- averageSpectraSingle(mzmlPth)

Viant-Metabolomics/msPurity documentation built on May 13, 2024, 8:23 a.m.