Dulce_AnnotateMS1: Annotate glycans in MS1 data

In margotbligh/Dulce: Annalyse and Annotate Glycans Mass Spectrometry Data

Annotate glycans in MS1 data

Description

This function constitutes the complete MS Data Annotation Pipeline. It is robust and smart enough to understand what kind of data is being inputed and continue the pipeline from the appropriate step. It is constructed in such a way that when an error occurs, the last correctly executed product is saved and returned.

Usage

Dulce_AnnotateMS1(
  data,
  cwp = NULL,
  pdp = NULL,
  names = NULL,
  classes = "Unclassified",
  perfwhm = 0.5,
  cor_eic_th = 0.75,
  polarity = NULL,
  rtmin = 0,
  rtmax = Inf,
  pgp = NULL,
  ppm = NULL,
  mzabs = NULL,
  output = "all"
)

Arguments

data	Object of any of these classes: MSnExp, OnDiskMSnExp, XCMSnExp, xcmsSet, xsAnnotate, data.frame.
cwp	CentWaveParam() object. If not given, default CentWaveParam() values are used.
pdp	PeakDensityParam() object. If not given, default PeakDensityParam() values are used.
names	Character vector with length equals to the amount of samples. It defines the identifier of each sample. If NULL (default), it generates names according to: sprintf('sample_\%03d', 1:nrow(data)) (sample_001, sample_002, etc).
classes	Character vector with length equals to the amount of samples. It defines the main grouping of the samples. If NULL (default), it defines an "Unclassified" group for all samples.
perfwhm	numeric value. It will be passed into CAMERA::groupFWHM() function.
cor_eic_th	numeric value. It will be passed into CAMERA::groupCorr() function.
polarity	character value, either "positive" or "negative". It will be passed into CAMERA::findAdducts() function.
rtmin	Numeric value specifying the lower retention time boundary.
rtmax	Numeric value specifying the higher retention time boundary.
pgp	predictGlycansParam() object. If not given, default predictGlycansParam() values are used.
ppm	M/z range for putative glycans in ppm units.
mzabs	M/z range for putative glycans in absolute units. Changed to NULL if both, ppm and mzabs, are specified.
output	Character object that determines what the function will return. If "main", a list with an 'XCMSnExp' object (if possible) and the last achieved product will be returned. If "all", a list with all the partial products along the pipeline is returned. If "last", only the last achieved product will be returned.

Value

If no errors occurs during the execution of the function, then the output depends on th output argument. If all, the function will return every partial product achieved. If main, XCMSnExp object (with peaks picked and grouped) and an annotated putative glycans data.frame are returned. If last, only the annotated putative glycans data.frame is returned. If an error occur during the execution of the function, it saves the last partial product achieved, and tries to return the specified output option.

Examples

# Examples have to be made with a toy data object.

margotbligh/Dulce documentation built on May 15, 2022, 10:51 a.m.