Man pages for jasenfinch/OrbiFIEmisc
Miscellaneous functions for the analysis of FIE-HRMS data.

accMassCollect accurate masses(5dp) for a given list of explanatory...
accMassFinalMake final accurate mass matrix from acc_mat using the most...
bordaCountBorda count of explanatory feature lists.
boxLinePlotboxLinePlot
boxPlotboxPlot
ClassificationClassification
colExpMassescollate all explanatory masses present in all lists.
corBascorBas
corFeaturescorrelation dendrogram of explanatory features based on all...
corrAnalysiscorrAnalysis
corVeccorVec
featRankfeatRank
featSelectionfeatSelection
featTabfeatTab
hcaPlothcaPlot
heatmapRatiosPlot heatmap of log2 ratios treatments
lda3dlda3d
ldaDotplotEigenvalue dotplot using ggplot2
ldaLoadingsldaLoadings
ldAnalysiswrapper function for LDA plotting, returns a list containg...
ldaPlotsLDA plots using ggplot2
ldaStripTwo class LDA plot using ggplot2
linePlotlinePlot
listsOrderOrder importance scores of feature lists
listsPreplistsPrep
listsPrepSigreturn lists of explanatory masses for each pairwise
listsSigChoose only significant features.
listsSpecSelect specific feature lists
logRatiologRatio
masterMatto build mean intensity matrices by class including nominal...
masterMixBuild mean intensity matrices by class.
meanShiftmeanShift
mfsmfs
occDropClass occupancy filtering.
occMatbuilds occupancy matrix by class
outDetchanged so that actual sample labels used
outlierDetoutlierDet
pca3dpca3d
pcaComppcaComp
pcaDotplotPCA variance dotplot using ggplot2
pcaLoadingspcaLoadings
pcAnalysiswrapper function for principle component analysis, returns a...
pcaPlotspca plots using ggplot2
plotBinPlot peak intensities for a 2dp mass bins for all classes
preProcFIE-HRMS data pre-processing
preProcesspreProcess
preprocSDpreprocSD
processDatprocessDat
reFormatClassireFormatClassi
removeSigremoveSig
rfImportancefunction to plot RF importance curves
runClassificationrunClassification
saveTabsaveTab
scaleSSto scale a vector to its sum of squares
selectionFrequencyFPRfalse positive approximation for random forest selection...
selectMethodpick out individual method from agg feature lists
shrinkListshrinkList
summaryDatsummaryDat
TICnormTotal Ion Count Normalisation.
unListunList
viewSpectrumview zoom able spectrum. double click to zoom out. 2 single...
jasenfinch/OrbiFIEmisc documentation built on May 17, 2017, 10:49 a.m.