annotate_matrix: Annotate matrix
In gbaquer3/rMSIcleanup: Anotation and removal of the matrix peaks in MALDI data

annotate_matrix

R Documentation

Annotate matrix

Description

Annotates the MS signals present in 'pks' related to the laser desorption/ionization promoting material used.

Usage

annotate_matrix(
  pks,
  matrix_formula,
  full_spectrum = NULL,
  normalization = "None",
  add_list = NULL,
  sub_list = NULL,
  max_charge = 1,
  analyzer_resolution = 20000,
  tol_mode = "scans",
  tol_ppm = 2e-04,
  tol_scans = 4,
  s_threshold = 0.65,
  s1_threshold = 0.8,
  s2_threshold = 0.8,
  similarity_method = "euclidean",
  correlation_method = "pearson",
  mag_of_interest = "intensity",
  min_multi = 1,
  max_multi = 10,
  detect_overlapping = T
)

Arguments

`pks`	Peak Matrix Image produced using rMSIproc
`matrix_formula`	String giving the chemical formula of the matrix in the enviPat notation#'
`full_spectrum`	Full spectrum before performing peak picking. It is used to give a higher degree of confidence to the S1 and S2 computation.
`normalization`	String indicating the normalization technique to use. Possible values: "None", "TIC","RMS", "MAX" or "AcqTic"
`add_list`	List of adducts to be added to the matrix formula in the format defined by enviPat. Example: c("H1","Na1","K1")
`sub_list`	List of compounds to be substracted to the matrix formula in the format defined by enviPat. Example: c("H1",H2O1")
`analyzer_resolution`	Analyzer resolution that is used to merge nearby peaks in-silico as the equipment would in real life
`tol_mode`	String determining the tolerance mode to be used when comparing the calculated masses with the experimental ones. "ppm": relative tolerance with respect to the calculated one in parts per million. "scans": Number of scans or datapoints present in the full spectrum -It is only applicable if full_spectrum is provided.
`tol_ppm`	Tolerance in parts per million. Only used if tol_mode="ppm".
`tol_scans`	Tolerance in number of scans. Only used if tol_mode="scans".
`s1_threshold`	Correlation between the theoretical and the real spectral pattern above which a given cluster is considered to be present
`s2_threshold`	Correlation between the spatial images of the peak in a cluster above which the peaks are included in the gold truth (gt)
`similarity_method`	Similarity method to be used in the computation of the distance
`mag_of_interest`	Magnitude of interest to use when performing the study. It can be "intensity" or "area".
`max_multi`	Maximum Cluster Multiplication. For each adduct -Adduct- it will generate a set of base formulas as follows: M+Adduct, 2M+Adduct, 3M+Adduct ... max_multi*M + Adduct
`s3_threshold`	Correlation between the spatial images of the peak in a cluster above which the peaks are included in the gold truth (gt)
`generate_pdf`	Boolean indicating whether to generate a TIFF figures or not
`default_page_layout`	Page layout to be used in the pdf plotting.
`folder`	Name of the folder in which to store the pdf report
`pks_i`	Index of the peak matrix
`plot_type`	String indicating the type of plot desired. Can have two possible values "debug" or "poster"
`include_summary`	Boolean value indicating if the summary is to be included in the pd