metaMS-package |
Analysis pipeline for MS-based metabolomics data |
addRI |
Add retention index information to an msp object |
alignmentLC |
LC alignment |
AnnotateFeature |
Annotate a Peaktable |
AnnotateTable |
Annotate a Peaktable |
annotations2tab |
Conversion of a list of annotation results into a table |
construct.msp |
Functions to handle msp-type objects (GC-MS) |
constructExpPseudoSpectra |
Create a list of all pseudospectra found in a GC-MS experiment of several samples. |
createSTDdbGC |
Create an in-house database for GC-MS annotation |
createSTDdbLC |
Create an in-house database for LC-MS annotation |
DB |
Information on three chemical standards measured in GC-MS (liquid injection) |
errf |
Mass error surface for Waters Synapt Q-TOF spectrometers |
exptable |
Sample table for the generation of a database of standards (LCMS) |
FEMsettings |
Example settings for 'metaMS' |
filter.msp |
Functions to handle msp-type objects (GC-MS) |
GCresults |
Results of metaMS for a small GC-MS data set |
generateStdDBGC |
Create an in-house database for GC-MS annotation |
generateStdDBLC |
Create an in-house database for LC-MS annotation |
getAnnotationLC |
Get LC annotation |
getAnnotationMat |
Obtain relative quantitative annotation results for GC-MS |
getFeatureInfo |
Construct an object containing all meta-information of the annotated pseudospectra (GC-MS). |
getPeakTable |
Extract a peak table from an xcms or CAMERA object |
LCDBtest |
Sample DB for LC-MS annotation |
LCresults |
Result metaMS for a small LC-MS data set |
LCxset |
Result metaMS for a small LC-MS data set |
makeAnnotation |
Conversion of a list of annotation results into a table |
match.unannot.patterns |
Compare pseudospectra across samples (GC-MS) |
match2ExtDB |
Match GC-MS spectra to an external reference DB |
matchExpSpec |
Match a GC-MS pseudospectrum to a database with a weighted crossproduct criterion. |
matchSamples2DB |
Match pseudospectra from several samples to an in-house DB (GC-MS) |
matchSamples2Samples |
Compare pseudospectra across samples (GC-MS) |
metaMS |
Analysis pipeline for MS-based metabolomics data |
metaMSsettings |
Class '"metaMSsettings"' |
metaMSsettings-class |
Class '"metaMSsettings"' |
metaSetting |
Get or set values in metaMSsettings objects |
metaSetting-method |
Get or set values in metaMSsettings objects |
metaSetting<- |
Get or set values in metaMSsettings objects |
metaSetting<--method |
Get or set values in metaMSsettings objects |
msp |
Functions to handle msp-type objects (GC-MS) |
peakDetection |
Wrapper for XCMS peak detection, to be used for both GC-MS and LC-MS data. |
plotPseudoSpectrum |
Plot a pseudospectrum. |
printInfo |
Functions for metaMS-formatted text output |
printString |
Functions for metaMS-formatted text output |
printWarning |
Functions for metaMS-formatted text output |
processStandards |
Process input files containing raw data for pure standards. |
read.msp |
Functions to handle msp-type objects (GC-MS) |
readStdInfo |
Read information of GC injections of standards from a csv file |
relInt |
Obtain relative quantitative annotation results for GC-MS |
removeDoubleMasses |
Remove double m/z entries in a pseudospectrum |
runCAMERA |
The CAMERA element in the metaMS pipeline |
runGC |
Wrapper for processing of GC-MS data files |
runLC |
Wrapper for processing of LC-MS data files |
show-method |
Class '"metaMSsettings"' |
smallDB |
Information on three chemical standards measured in GC-MS (liquid injection) |
stdInfo |
Information on three chemical standards measured in GC-MS (liquid injection) |
Synapt.NP |
Example settings for 'metaMS' |
Synapt.RP |
Example settings for 'metaMS' |
threeStdsDB |
Information on three chemical standards measured in GC-MS (liquid injection) |
threeStdsInfo |
Information on three chemical standards measured in GC-MS (liquid injection) |
threeStdsNIST |
Information on three chemical standards measured in GC-MS (liquid injection) |
to.msp |
Functions to handle msp-type objects (GC-MS) |
treat.DB |
Scaling of pseudospectra in an msp object |
TSQXLS.GC |
Example settings for 'metaMS' |
write.msp |
Functions to handle msp-type objects (GC-MS) |
xset2msp |
Functions to handle msp-type objects (GC-MS) |