compute.Priors: Computing prior probabilities associated with putative...

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

Computing prior probabilities associated with putative annotations

Description

This functions takes as input the output of the find.hits() function and computes the prior probabilities for the putative annotations

Usage

compute.Priors(Hits, dataset, pk = rep(1, nrow(Hits$all.formulas)), ppm,
  unknown.ppm = NA, RT.pen = 0.5, v = T, IT = 120,
  pr.lim = 1e-05)

Arguments

Hits	The output of find.hits() function
dataset	A matrix containing the measured data, organized in 3 colums: mz, RT and Int
pk	A vector of length nrow(Hits$all.formulas). Values between 0 and 1 expressing initial confidence of the presence of each formula
ppm	A number indicating the instrument accuracy to be considered
unknown.ppm	The ppm number to be assigned to unknown (default NA - No unknown is considered)
RT.pen	A numerical value indicating the multiplicative factor used when the measured retention time is outside of the range reported in the database
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)
pr.lim	A number inidicating the lowest probability value allowed (default 1e-05)

Value

A list containing the matrix of the prior probabilities and the id.masses and all.formulas objects

Author(s)

Francesco Del Carratore [e-mail]

See Also

find.Hits IPAposteriors

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