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

View source: R/purityD-av-spectra.R

averageSpectraSingleR Documentation

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)

computational-metabolomics/msPurity documentation built on April 19, 2022, 10:21 a.m.