retcor-methods {xcms}R Documentation

Align retention times across samples

Description

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
method 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, method = c("loess", "linear"), span = .2, family = c("gaussian", "symmetric"), plottype = c("none", "deviation", "mdevden"), col = NULL, ty = NULL)

See Also

xcmsSet-class, loess


[Package xcms version 1.14.1 Index]