retcor.peakgroups-methods {xcms} | R Documentation

## 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`

[Package xcms version 3.0.2 Index]