averageSpectra-purityD-method: Using purityD object, calculates to average mz, intensity and...

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

Using purityD object, calculates to average mz, intensity and signal-to-noise of multiple scans from multiple MS datafiles (mzML or .csv)

Description

Uses a purityD object with references to multiple MS files. For each file: Averages multiple scans together, see averageSpectraSingle for more information

Usage

## S4 method for signature 'purityD'
averageSpectra(
  Object,
  rtscn = "all",
  scanRange = NA,
  timeRange = NA,
  clustType = "hc",
  ppm = 1.5,
  snthr = 3,
  av = "median",
  missingV = "zero",
  minfrac = 0.6667,
  normTIC = FALSE,
  snMeth = "median"
)

Arguments

Object	object; purityD object
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
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
normTIC	boolean; If TRUE then RSD calculation will use the normalised intensity (intensity divided by TIC) if FALSE will use standard intensity
snMeth	character; Type of snMethod to use ['mean', 'median', 'precalc']. Precalc only applicable when using the csvFile parameter as TRUE

Value

purityD object with averaged spectra

See Also

averageSpectraSingle

Examples

datapth <- system.file("extdata", "dims", "mzML", package="msPurityData")
inDF <- Getfiles(datapth, pattern=".mzML", check = FALSE, cStrt = FALSE)
ppDIMS <- purityD(fileList=inDF, cores=1, mzML=TRUE)
ppDIMS <- averageSpectra(ppDIMS)

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