find.hits: Finding putative annotations

In francescodc87/IPA: Integrated Probabilistic Annotation (IPA) method for mass spectrometry data

Finding putative annotations

Description

This function finds all the possible annotations given an user-defined ppm window.

Usage

find.hits(adducts.matrix, dataset, ppm.thr, RTwin, isotopes,
  iso.threshold = 1, corr.matrix = NULL, corr.thr = 0.75,
  relation.id = NULL, v = T, IT = 500)

Arguments

adducts.matrix	A matrix contains information about all possible adducts. Columns are: KEGG.id (e.g. 'C00002'), adduct (e.g. 'M+H'), RT (previously known retention time for the compound, NA if unknown), formula (e.g. C10H17N5O13P3), theoretical mz (e.g. 508.003570124), charge (e.g. -1) mono ('mono' if monoisotopical form, 'iso' otherwise)
dataset	A matrix containing the measured data, organized in 3 colums: mz, RT and Int
ppm.thr	A numerical value indicating the maximum accuracy value to be considered
RTwin	A numerical value indicating the maximum difference allowed between measured RT of different isotopes
isotopes	A matrix containing infomation about isotopes
iso.threshold	A numerical value indicating the probability below which isotope peaks can be omitted
corr.matrix	A matrix containing the correlation values between peaks
corr.thr	A numerical value expressing the treshold used to consider the correlations significant
relation.id	A vector containg class labels of the previously grouped peaks
v	A logical value indicating if the progress will be shown (default TRUE)
IT	A number inticating after how many iteration an update should be shown (default 120)

Value

A list containing the matrix of the posterior probabilities, the id.masses vector, the all.formulas dataframe and the allsampcomp matrix containing all the assignments for each iteration of the Gibbs sampler

Author(s)

Francesco Del Carratore [e-mail]

See Also

find.Hits IPAposteriors

francescodc87/IPA documentation built on April 7, 2023, 4:27 a.m.