Man pages for lauzikaite/massFlowR
LC-MS Data Pre-Processing

addERRSAdd peak matching error windows using user-defined _m/z_ and...
adjustBATCH-massFlowTemplate-methodadjustBATCH
alignPEAKS-massFlowTemplate-methodAlign peaks detected in LC-MS samples using spectral...
annotateDS-massFlowAnno-methodAnnotate dataset using chemical reference database.
assignCOSAssign dataset's peak-groups to template peak-groups based on...
buildANNOBuild a 'massFlowAnno' class object.
buildDBBuild a chemical reference database table using rda files
buildGRAPHBuild a correlation network of peaks
buildTMPBuild a sample alignment and annotation template
buildVECTORBuild a vector for a peak-group using peaks _m/z_ and...
checkANNOTATION-massFlowAnno-methodCheck annotation results between selected database chemical...
checkFILECheck and load file for peak alignment
cleanPEAKSClean peak table from duplicating peaks
comparePCS-massFlowAnno-methodCompare selected pseudo chemical spectra.
corEICObtain EIC correlation between two peaks
corPEAKSCorrelate two peaks' intensities across all samples.
do_alignPEAKSAlign dataset's and template peaks using dot-product...
do_groupPEAKSGroup peaks of a single LC-MS spectrum using EIC correlation
exportPEAKExport centWave measures for a peak-of-interest in every...
exportSAMPLEExtract centWave values for peaks in the final template for a...
extractCOMMUNITIESExtract communities, or, Pseudo Chemical Spectra, with > 1...
extractEICObtain extracted ion chromatograms for all picked peaks
extractINTExtract raw signal values for defined mz and rt region.
extractMISSExtract samples with missed peaks, for which intensity have...
extractPEAKGRExtract peak-group data from every sample
filepath-massFlowTemplate-methodObtain the absolute path to metadata file of the experiment
fillPEAKS-massFlowTemplate-methodFill peaks
fillSAMPLEFill intensity values for peaks missed in the...
findANNOchemid-massFlowAnno-methodFind annotations for selected chemical compound id
findANNOpcs-massFlowAnno-methodFind annotations for selected pseudo chemical spectra
getCORmatBuild a correlation matrix between peaks-of-interest
getCOSmatEstimate cosine angles between the vectors representing...
getINTGet intensity of a peak-of-interest in a single sample.
getMATCHESGet template peaks that match the target peak by _m/z_ and...
getPEAKIDSExtract peakids from every community/Pseudo Chemical Spectra...
getPEAKmediansGet median centWave measures for a peak-of-interest across...
getRTbinsSplit a dataset-of-interest and template into _rt_ regions...
groupPEAKSGet peak-groups representing different chemical spectra in...
groupPEAKS_paralPerform peak-picking and grouping into Extracted Chemical...
loadALIGNEDBuild sample alignment and annotation template using already...
massFlowAnno-classmassFlowAnno, a class for peak table annotation with a...
massFlowR-packagemassFlowR: a package for pre-processing of high-resolution,...
massFlowTemplate-classmassFlowTemplate, a class for sample alignment and annotation
modelPEAKSFunction models intensity integration values for missing...
normSPECNormalise a vector representing peaks' intensity values to...
orderBYrtOrder a peak table by variables' _rt_
peaksVALIDATED-massFlowTemplate-methodCheck if massFlowTemplate object was validated
pickPEAKSPeak detection using the centWave method
rankCOSRank cosines, assigning 1 to the highest cosine and 0s to...
rbindCLEANBind a list of data frames
readDATARead raw LC-MS data into memory
scaleEDGESScale correlation coefficients
smoothVALUEHelper function to model intensity integration values for...
validFILECheck the validity of a raw LC-MS file.
validPEAKGRValidate a peak-group-of-interest by performing a...
validPEAKS-massFlowTemplate-methodValidate aligned peaks and their corresponding peak-groups
lauzikaite/massFlowR documentation built on Sept. 10, 2019, 10:21 p.m.