Classic alignment methods such as in the popular XCMS package often assume a single time-warping function for each sample.  The ncGTW software tool is developed currently as a plug-in to detect and realign misaligned features present in standard XCMS output.



XCMS
Here, we describe an integrated reference-free profile alignment method, neighbor-wise compound-specific Graphical Time Warping (ncGTW), that can detect misaligned features and align profiles by leveraging expected RT drift structures and compound-specific warping functions.  Specifically, ncGTW uses individualized warping functions for different compounds and assigns constraint edges on warping functions of neighboring samples.  Validated with both realistic synthetic data and internal quality control samples, ncGTW applied to two large-scale metabolomics LC-MS datasets identifies many misaligned features and successfully realigns them.  The ncGTW software tool is developed currently as a plug-in to detect and realign misaligned features present in standard XCMS output.


 An R package of ncGTW is freely available at Bioconductor and https://github.com/ChiungTingWu/ncGTW. 
ncGTW
An R package of ncGTW is freely available at Bioconductor and https://github.com/ChiungTingWu/ncGTW. 
R package
An R package of ncGTW is freely available at Bioconductor and https://github.com/ChiungTingWu/ncGTW. 
Bioconductor
An R package of ncGTW is freely available at Bioconductor and https://github.com/ChiungTingWu/ncGTW. 
GitHub