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

## Documentation for package ‘ncGTW’ version 1.12.0

- 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