ncGTWparam-class: Class "ncGTWparam"

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

Description

An S4 class for storing the needed paramters of ncGTW alignment.

Details

This function initializes the needed paramters of ncGTW alignment with defaults, so this function could be called without any input. The alignment should be fine with all default parameters. If the computing time is an issue, the user could consider increase downSample and/or decrease stpRat for a faster speed. If the alignment result is not good enough, one can consider increase strNum and/or diaNum to integrate more neighboring information to increase the quality of alignment, but the speed may drop.

Slots

downSample

A factor of downsampling. The larger, the faster speed of alignment, but the accuracy may decrease. The default is 2.

stpRat

A factor to control the maximum RT shift of a point in alignment, and the maximum shift is determined by stpRat * "The RT range of the feature". If maxStp is set, then stpRat would be neglected. The default is 0.6.

maxStp

A value determines the maximum RT shift of a point in ncGTW alignment. If the user wants to decide the maximum shif by the RT range of the feature, this argument should be NaN. The default is NaN.

strNum

A value controls how many neighboring warping functions are connected to each warping function in ncGTW graph. There are two samples corresponding to a warping function, and at least one sample should be the same in another warping function to be considered as a neighbor controlled by strNum.

diaNum

A value controls how many neighboring warping functions are connected to each warping function in ncGTW graph. There are two samples corresponding to a warping function, and the two samples could also be different to another warping function to be considered as a neighbor controlled by diaNum.

nor

A value controls p-norm to compute the distance between the points on the profiles, and the default is 1 (Manhattan norm).

ncGTW documentation built on Nov. 8, 2020, 8:08 p.m.