simpleIPA: Single function for the whole IPA analysis

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

Single function for the whole IPA analysis

Description

Wrapper summmarizing the whole IPA analysis in one single function. USE IT CAREFULLY!

Usage

simpleIPA(dataset, adducts.matrix, DB, ionisation, ppm, ppm.thr, RTwin,
  isotopes, iso = TRUE, add = TRUE, bio = TRUE, ints = TRUE,
  rt = TRUE, iso.threshold = 1, corr.matrix = NULL,
  corr.thr = 0.75, relation.id = NULL, pk = NULL, delta.bio = 1,
  delta.add = 1, delta.iso = 1, allsampcomp = NULL,
  ratio.toll = 0.8, allsamp = FALSE, no.its = 1100, burn = 100,
  RT.win.post = 3, IDs = NULL, unknown.ppm = NA, RT.pen = 0.5,
  pr.lim = 1e-05, fully.connected = FALSE, ratios = TRUE,
  connection.type = "reactions", connections = NULL, v = T,
  IT = 500)

Arguments

dataset	A matrix containing the measured data, organized in 3 colums: mz, RT and Int
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)
DB	The database used in a dataframe format. It has to be organized in the same fashion of the one included with the package
ionisation	A character indicating the ionisation mode of the experiment, either 'positive' or 'negative'
ppm	A number indicating the instrument accuracy to be considered
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	A logical parameter. If true isotope connections are used
add	A logical parameter. If true adducts connections are used
bio	A logical parameter. If true biochemical connections are used
ints	A logical parameter. If true intensities are used
rt	A logical parameter. If true RTs are used for filtering connections
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
pk	A vector of length nrow(adducts.matrix). Values between 0 and 1 expressing initial confidence of the presence of each formula
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)
RT.win.post	A numerical value expressing the maximum Retention time difference allowed between adducts/isotopes
IDs	name of each feature in the initial dataset
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
pr.lim	A number inidicating the lowest probability value allowed (default 1e-05)
fully.connected	A logical value if TRUE all adducts will be considered connected with each other, if FALSE (default) all the adducts are only connected to the main adduct
ratios	A logical value indicating if the matrix should contain the expected intensity ratios (default TRUE)
connection.type	if equal to "reactions" (default) considers the reactions reported in the database. If it is equal to "formulas", the function consider the list of possible reactions reported in connections
connections	if connection.type=="fomulas", this vector contains a list of formulas that are likely to be added or substracted by an enzymatic reaction. If it is equal to NULL the default list of formulas is used
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 Hits, Prior, Post and parsed results

Author(s)

Francesco Del Carratore [e-mail]

See Also

find.Hits compute.Priors IPAposteriors

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