MAIT (version 1.6.0)

sigPeaksTable: Build a table of the information related to the significant features contained in a MAIT object

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

See Also

spectralTStudent spectralAnova

Examples

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