sigPeaksTable: Build a table of the information related to the significant...

In MAIT: Statistical Analysis of Metabolomic Data

Description

Function sigPeaksTable takes an MAIT-class object containing significant feature information and builds a table with the information related to these features.

Usage

sigPeaksTable(MAIT.object=NULL,
             printCSVfile=FALSE,
             extendedTable = TRUE,
             printAnnotation=TRUE)

Arguments

MAIT.object	A MAIT-class object where significant features have already been found.
printCSVfile	Set to TRUE if an output table has to be produced. The table should be found in (working directory)/(project directory)Tables/significativeFeatures.csv.
extendedTable	Set to TRUE the table created by the peak external data is used.
printAnnotation	Set to TRUE The peak annotation is provided in the output table

Value

A table containing:

• First column (mz): Peak mass

• Second column(mzmin): Minimum peak mass of the peak group.

• Third column(mzmax): Maximum peak mass of the peak group.

• Fourth column(rt): Peak retention time (in minutes).

• Fifth column(rtmin): Minimum peak retention time of the peak group.

• Sixth column(rtmax): Maximum peak retention time of the peak group.

• Seventh column(npeaks): Number of samples where the peak has been detected.

• The columns from the nineth to the column labeled "isotopes" contain number of class samples where the peak has been detected and the intensities of the peak among samples.

• The isotopes column shows if the peak has been identified as a possible isotope.

• The adduct column shows which kind of adduct could the peak be.

• The column labeled pcgroup contains the spectral ID of the peak.

• The P.adjust column contains the corrected peak p-value using post-hoc methods.

• The p column shows the peak p-value with no multiple test correction.

• The Fisher column shows the Fisher test results for the peak. Each of the letters separated by the character "_" corresponds to a class value. Classes having the same letters are indistinguible whereas those having different letters are statistically different clases.

• The last columns contain the mean and median values for each feature

Author(s)

Francesc Fernandez, [e-mail]

See Also

spectralTStudent spectralAnova

Examples

data(MAIT_sample)
MAIT<-spectralSigFeatures(MAIT,p.adj="fdr",parametric=TRUE)
head(sigPeaksTable(MAIT))

MAIT documentation built on Nov. 8, 2020, 5:43 p.m.