Description Usage Arguments Details Value See Also
View source: R/xcmsWarpgroup.R
group.warpgroup
returns an xcmsSet with the original groups and peaks replaced by those returned by the warpgroup
algorithm.
1 2 3 4 | group.warpgroup(xs, xr.l, rt.max.drift, ppm.max.drift, rt.aligned.lim, smooth.n,
normalize = T, eic.resample.target = Inf, output.groups = F,
sc.aligned.factor = 1, detailed.groupinfo = F, min.peaks = 1,
pct.pad = 0.1)
|
xs |
An xcmsSet object with initial grouping information. |
xr.l |
A list contanining xcmsRaw objects for each sample in the xcmsSet object in order. |
rt.max.drift |
Float. The maximum retention time drift in seconds expected for a peak in the data set in scans. Used when setting the boundaries for looking for missing peaks. |
ppm.max.drift |
Integer. The maximum mass drift expected for a peak in the data set in ppm. Used when setting the boundaries for looking for missing peaks. |
rt.aligned.lim |
Float. Peak bounds after alignment are considered to describe the same region if they are within this limit. |
smooth.n |
Number of points to consider for the moving average smoothing of each EIC. 1 disables smoothing. See |
normalize |
Boolean. If TRUE all EICs will be normalized to 1. See |
eic.resample.target |
If less than one the resulting EICs will be of length max*length.target. If greater than 1 resulting EICs will be of length length.target. If Inf resulting EICs will be of length max. See |
output.groups |
Boolean. If |
sc.aligned.factor |
Float. Experimental feature where graph edges are weighted proportionally to the distance be tween the aligned peak bounds. Higher numbers emphasize closer peak bounds. |
detailed.groupinfo |
Boolean. Returns several extra descriptors of the warping and graph clustering. |
min.peaks |
Integer. Groups with fewer peaks than |
This function simply iterates over each group in the xcmsSet and runs warpgroup
on them. The resulting warpgroup output is then re-integrated and returned as a new xcmsSet.
The resulting xcmsSet is ready for a call to diffreport
and does not need to be grouped. The results will be redundant and should be filtered appropriately.
An xcmsSet with groups and peaks replaced by warpgroup generated ones.
See https://github.com/nathaniel-mahieu/warpgroup for examples.
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