IPAposteriors: Computing Posterior probabilities associated with putative...

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

Computing Posterior probabilities associated with putative annotations

Description

This functions takes as input the output of the compute.Priors() function and estimates the posterior probabilities for the putative annotations

Usage

IPAposteriors(P, Add = NULL, Iso = NULL, Bio = NULL, Int = NULL,
  delta.bio = 1, delta.add = 1, delta.iso = 1, allsampcomp = NULL,
  ratio.toll = 0.8, allsamp = FALSE, no.its = 1100, burn = 100,
  Corr.matrix = NULL, corr.thr = 0.8, RT = NULL, RT.win = 3,
  rel.id = NULL, v = TRUE, IT = 500)

Arguments

P	The output of compute.Priors() function
Add	A binary matrix containing all the possible adducts connections
Iso	A matrix containg the expected intensity ratios between the considered isotopes
Bio	A binary matrix containing the the possible biochemical connections
Int	A numerical vector containing the measure intensities
delta.bio	A number expressing the confidence on the information encoded in Bio (smaller the value higher the confidence)
delta.add	A number expressing the confidence on the information encoded in Add (smaller the value higher the confidence)
delta.iso	A number expressing the confidence on the information encoded in Iso (smaller the value higher the confidence)
allsampcomp	A matrix containing all the assignments for each iteration of the Gibbs sampler in a previus run
ratio.toll	A numerical value expressing the minimum accepeted ratio between thereoretical and observed intensity ratios between isotopes (default 0.8)
allsamp	A logical value indicating if the output should contain the allsampcomp object
no.its	A numerical value indicating the number of iterations the to be performed by the Gibbs sampler (default 1100)
burn	A numerical value indicating the number of initial iterations to be ignored when computing the posterior probabilities (default 100)
Corr.matrix	A matrix containing the correlation values between peaks
corr.thr	A numerical value expressing the treshold used to consider the correlations significant
RT	A numerical vector containin the measured retention times
RT.win	A numerical value expressing the maximum Retention time difference allowed between adducts/isotopes
rel.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 compute.Priors

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