retcor.peakgroups-methods: Align retention times across samples

In xiaodfeng/DynamicXCMS: LC-MS and GC-MS Data Analysis

Align retention times across samples

Description

These two methods use “well behaved” peak groups to calculate retention time deviations for every time point of each sample. Use smoothed deviations to align retention times.

Arguments

object	the xcmsSet object
missing	number of missing samples to allow in retention time correction groups
extra	number of extra peaks to allow in retention time correction correction groups
smooth	either "loess" for non-linear alignment or "linear" for linear alignment
span	degree of smoothing for local polynomial regression fitting
family	if gaussian fitting is by least-squares with no outlier removal, and if symmetric a re-descending M estimator is used with Tukey's biweight function, allowing outlier removal
plottype	if deviation plot retention time deviation points and regression fit, and if mdevden also plot peak overall peak density and retention time correction peak density
col	vector of colors for plotting each sample
ty	vector of line and point types for plotting each sample

Value

An xcmsSet object

Methods

object = "xcmsSet"

retcor(object, missing = 1, extra = 1, smooth = c("loess", "linear"), span = .2, family = c("gaussian", "symmetric"), plottype = c("none", "deviation", "mdevden"), col = NULL, ty = NULL)

See Also

xcmsSet-class, loess retcor.obiwarp

xiaodfeng/DynamicXCMS documentation built on Aug. 6, 2023, 3:02 p.m.