Alignment of LC-MS Profiles by Neighbor-wise Compound-specific Graphical Time Warping with Misalignment Detection

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Documentation for package ‘ncGTW’ version 1.19.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

ncGTW-package	ncGTW: A package for detecting and aligning the misaligned features in LC-MS data
adjustRT	Adjust retention time
alignData	ncGTWoutput-accessors
alignData-method	ncGTWoutput-accessors
compCV	Compare CV
downSample	ncGTWinput-accessors
downSample-method	ncGTWinput-accessors
fillPeaksChromPar	Edited XCMS fillPeaksChromPar for feature-wise warping functions
getPeaksncGTW	Edited XCMS getPeaks for feature-wise warping functions
groupInfo	ncGTWinput-accessors
groupInfo-method	ncGTWinput-accessors
loadProfile	Load sample profiles for each peak group
meanCorOl	Compute average pairwise correlation and overlapping area
misalignDetect	Detect misaligned peak groups in xcmsSet object of XCMS
ncGTW	ncGTW: A package for detecting and aligning the misaligned features in LC-MS data
ncGTWalign	Run ncGTW alignment
ncGTWinput	Class "ncGTWinput"
ncGTWinput-class	Class "ncGTWinput"
ncGTWoutput	Class "ncGTWoutput"
ncGTWoutput-class	Class "ncGTWoutput"
ncGTWparam	Class "ncGTWparam"
ncGTWparam-class	Class "ncGTWparam"
ncGTWpath	ncGTWinput-accessors
ncGTWpath-method	ncGTWinput-accessors
ncGTWpeaks	ncGTWwarp-accessors
ncGTWpeaks-method	ncGTWwarp-accessors
ncGTWwarp	Class "ncGTWwarp"
ncGTWwarp-class	Class "ncGTWwarp"
plotGroup	Plot profiles for each peak group
profiles	ncGTWinput-accessors
profiles-method	ncGTWinput-accessors
rtncGTW	ncGTWwarp-accessors
rtncGTW-method	ncGTWwarp-accessors
rtRaw	ncGTWinput-accessors
rtRaw-method	ncGTWinput-accessors
scanRange	ncGTWinput-accessors
scanRange-method	ncGTWinput-accessors
xcmsExamples	Examples of xcmsSet for inputs of ncGTW