group.warpgroup: A wrapper for supplying xcmsSet objects to Warpgroup.

In nathaniel-mahieu/warpgroup: Advanced Alignment, Grouping, and Consensus Peak Bounding of LC/MS Data

Description

group.warpgroup returns an xcmsSet with the original groups and peaks replaced by those returned by the warpgroup algorithm.

Usage

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)

Arguments

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 eicMatFromList
normalize	Boolean. If TRUE all EICs will be normalized to 1. See eicMatFromList
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 eicMatFromList
output.groups	Boolean. If TRUE the output is a list of warpgroup outputs for every group rather than an xcmsSet. Allows for better integration parameter selection with warpgroupsToXs.
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 min.peaks are skipped.

Details

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.

Value

An xcmsSet with groups and peaks replaced by warpgroup generated ones.

See Also

See https://github.com/nathaniel-mahieu/warpgroup for examples.

nathaniel-mahieu/warpgroup documentation built on May 23, 2019, 12:19 p.m.