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flagme (version 1.28.0)

Analysis of Metabolomics GC/MS Data

Description

Fragment-level analysis of gas chromatography - mass spectrometry metabolomics data

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Version

Version

1.28.0

License

LGPL (>= 2)

Maintainer

Mark Robinson

Last Published

February 15th, 2017

Functions in flagme (1.28.0)

exportSpectra

exportSpectra
multipleAlignment-class

Data Structure for multiple alignment of many GCMS samples
normDotProduct

Normalized Dot Product
parseChromaTOF

Parser for ChromaTOF files
parseELU

Parser for ELU files
plot.peaksDataset

Plotting functions for GCMS data objects
addXCMSPeaks

Add xcms/CAMERA peak detection results
eitherMatrix-class

The eitherMatrix class
retFatMatrix

retFatMatrix
correlationAlignment-class

"correlationAlignment-class"
peaksAlignment-class

Data Structure for pairwise alignment of 2 GCMS samples
compress

Compress an alignment object
plotSpectra

plotSpectra
addAMDISPeaks

Add AMDIS peak detection results
gatherInfo

Gathers abundance informations from an alignment
progressiveAlignment-class

Data Structure for progressive alignment of many GCMS samples
calcTimeDiffs

Calculate retention time shifts from profile alignments
betweenAlignment

Data Structure for "between" alignment of many GCMS samples
rmaFitUnit

Fits a robust linear model (RLM) for one metabolite
addChromaTOFPeaks

Add ChromaTOF peak detection results
imputePeaks

Imputatin of locations of peaks that were undetected
plotImage

Plot of images of GCMS data
correlationAlignment

Function for correlation-based alignment strategy of multiple GCMS samples
clusterAlignment

Data Structure for a collection of all pairwise alignments of GCMS runs
dp

Dynamic programming algorithm, given a similarity matrix
peaksDataset

Data Structure for raw GCMS data and peak detection results